At first, the offer seemed generous. Erica Sklar was in a homeless shelter and needed a more stable place to live. Victor Rivera, who oversaw a network of shelters, including the one where she was staying, said he had a solution: a spare apartment for her at his home in the Bronx.

But after Ms. Sklar moved in, she said, she realized that Mr. Rivera, whose nonprofit organization is one of the largest operators of homeless shelters in New York, had other intentions. In December 2016, he asked to see a leaking ceiling in her bedroom, then turned off the lights, pushed her against a wall and began fondling her, according to Ms. Sklar and two friends in whom she confided.

He demanded she give him oral sex, suggesting he would evict her if she refused, she said. Desperate to hold on to her apartment, she complied.

Ms. Sklar is one of 10 women who said they had endured assault or unwanted sexual attention from Mr. Rivera, The New York Times found. Even as some women have sounded warnings about Mr. Rivera — including two who were given payments by his organization that ensured their silence — his power and influence have only grown during New York’s worst homeless crisis in decades.

His organization, the Bronx Parent Housing Network, has received more than $274 million from the city to run homeless shelters and provide services just since 2017. The pandemic has intensified Mr. Rivera’s importance: As the coronavirus swept through the homeless population, the city gave his group $10 million to provide rooms where infected people could isolate and recover.

Women reported Mr. Rivera’s behavior to a state agency, a city hotline and, in one instance, the police. But he maintained his perch atop the organization.

One employee of the Bronx Parent Housing Network said that Mr. Rivera, the chief executive, forced her to give him oral sex in 2016 and then fired her, according to police records, interviews and other documents. In 2018, another employee accused Mr. Rivera of groping her and whispering sexual comments in her ear. After both women separately complained to a state human rights agency, the Bronx Parent Housing Network paid them a total of $175,000 in settlements that prohibited them from speaking publicly about their allegations, according to interviews and records reviewed by The Times.

Five of the women were living in Mr. Rivera’s homeless shelters, or had recently left, when Mr. Rivera approached them for sex, they said.

“He’s got a lot of power over a lot of vulnerable girls,” said Ms. Sklar, 49.

On Thursday, after The Times asked the Bronx Parent Housing Network about the accusations of sexual misconduct, the organization put him on leave and, at the city’s direction, moved to hire an independent investigator to examine the allegations. Mr. Rivera, 60, declined to answer any specific questions but issued a statement denying wrongdoing.

“I have always treated the women I work with at B.P.H.N. with dignity and respect. These allegations are unfair, baseless and without merit,” Mr. Rivera said in the statement. He said he was confident that the investigation would clear him and he looked forward to returning to work.

It was a rare moment of reckoning for Mr. Rivera after a decade of acting with near impunity, The Times found.

More than 78,000 people in New York City are homeless, a number that has risen to record highs in recent BDSM years and threatens to grow as the city suffers the full economic fallout from the pandemic. New York City is under an unusual and longstanding court order to provide temporary shelter to every homeless person, and it relies on dozens of nonprofit groups like the Bronx Parent Housing Network to manage shelters and help people secure permanent housing.

Last year alone, the city awarded more than $2.1 billion to these groups.

Despite this soaring spending, officials are slow to punish organizations that break the rules. In New York, a city with some of the highest real estate values in the country, officials say there is a limited number of nonprofits willing and able to run shelters.

The allegations against Mr. Rivera, which have not been previously disclosed, show the extent to which shelter providers can avoid meaningful repercussions for even serious malfeasance, a Times investigation found.

As the city’s housing crisis worsened and his organization flourished, Mr. Rivera treated his nonprofit less as a charity and more as his personal empire. He has given jobs to family members, entangled his for-profit businesses with his nonprofit, awarded contracts to close associates and enjoyed new trappings of wealth: He drove a Mercedes-Benz leased by his organization and bought a home with a heated pool north of New York City and another house in the Poconos.

“He walks about as if he’s untouchable,” said Vanessa Anderson, a former payroll accountant who left the nonprofit in 2018 and said Mr. Rivera had made sexually inappropriate comments to her.

City officials knew about some of Mr. Rivera’s financial irregularities — a whistle-blower complained about nepotism and conflicts of interest in 2017 — but still poured millions into the organization. One homeless woman told the New York Department of Social Services, which oversees shelter providers, that she had been harassed by Mr. Rivera, but the department simply passed her grievance to his organization to investigate.

To piece together the story of Mr. Rivera, The Times interviewed more than 50 current and former employees and more than a dozen women who lived in shelters run by the Bronx Parent Housing Network, and examined hundreds of pages of contracts, confidential settlement agreements, lawsuits, tax records and internal financial documents from the organization.

The Department of Social Services said it had made repeated efforts to keep the management of the Bronx Parent Housing Network on “the straight and narrow” but in general tried to avoid ending contracts with shelter providers.

“We have a legal and moral obligation to provide shelter to all those who need it, no matter what, and our first objective is therefore to resolve matters collaboratively,” a spokesman for the department, Isaac McGinn, said. Still, he said, the city would hold shelter operators accountable.

The department has referred The Times’s findings about Mr. Rivera’s financial entanglements to investigators, he said. “These additional allegations about the C.E.O.’s personal behavior are also extremely troubling and, if true, will not be tolerated,” he said.

Before The Times presented the Bronx Parent Housing Network with the allegations of sexual assault and harassment, the organization defended Mr. Rivera’s management. Through a lawyer, the group denied any fiscal impropriety, as did Mr. Rivera. He said in his statement that he had little business experience when he started the organization and had worked with the city to make it more professional.

“I have never wanted anything more than to give back to this city and help the many people who need it,” Mr. Rivera said, “because I was once one of those people.”

Mr. Rivera frequently invokes his own story of homelessness and addiction, saying that he spent much of his early childhood in a shelter and a poor neighborhood in the South Bronx. He was selling drugs at age 9, he has said in media interviews.

Before he was even old enough for a learner’s permit, he had made so much money dealing drugs that he had bought himself a couple of cars, he said in an interview in 2019 with “Realty Speak,” a housing podcast. He said he fathered a child at 15, then, in the throes of an addiction to crack cocaine, he became homeless, was incarcerated for drug possession, and later served a brief stint in state prison from 1989 to 1990 for violating probation.

After his release, he said, he vowed to change his life and quit drugs. He became involved with a group to provide low-income housing and worked with recovering drug addicts, according to a copy of his résumé. “I continue to do what I do to help society and pay that forward,” he said on the podcast.

He helped to found the Bronx Parent Housing Network in 2000 with others from his church, and focused on providing housing and services for homeless people and those with H.I.V. and AIDS. For years, the nonprofit scrambled for funding. In 2012, the year before Bill de Blasio was first elected mayor, the organization brought in $1.1 million in revenue, tax filings show. Mr. Rivera’s salary was $67,000.

An explosion in New York’s homeless population changed the group’s fortunes, and Mr. Rivera’s. Mr. de Blasio pledged to revamp the shelter system and in 2017 announced that the city would open 90 new sites. Nonprofit organizations, including the Bronx Parent Housing Network, applied to fill the demand.

Mr. Rivera was by then married to a woman also involved in homeless housing efforts in the Bronx. The couple became regulars at charity functions and Bronx political events and hosted a campaign fund-raiser for Ritchie Torres, a councilman who was elected to Congress last year, according to former staff members and an event invitation obtained by The Times. Since 2010, Mr. Rivera and his wife, Lanet Rivera, have donated more than $35,000 to local officials, campaign-finance records show.

The political contacts have been a boon to the Bronx Parent Housing Network: The group has received more than $1 million in City Council discretionary funding, a pool of money that council members award to favored nonprofit organizations, records show. Much of it has come from Mr. Torres, who also vouched for Mr. Rivera’s organization with city homeless officials.

Mr. Torres declined to comment on Mr. Rivera’s campaign contributions or the fund-raiser. In a statement, he said he relied on a host of city agencies to vet shelter providers.

“Not one of them raised a red flag,” Mr. Torres said.

As city contracts came in, Mr. Rivera’s salary swelled — to more than $306,000 in 2019, tax filings show — and he surrounded himself with opulence. He bought a $780,000 home with a heated pool and a waterfall in Stony Point, N.Y., and a four-bedroom house in the Poconos, according to property records. On Facebook, his wife showed off a lavish birthday gift he bought her: a Celine Phantom handbag that retailed for at least $2,100. His organization also provided a Mercedes-Benz E-Class sedan for him with a vanity license plate touting the charity: BPHN ORG.

The Bronx Parent Housing Network said that it had leased the Mercedes-Benz for Mr. Rivera to use at special events and that it was a cheaper alternative to other vehicles the organization had considered. Mr. Rivera purchased the car outright while The Times was reporting this story, and the nonprofit said it no longer leased vehicles for executives.

By 2019, the organization’s annual revenue had grown to more than $81 million, internal records show. It now oversees about 68 housing sites.

Ms. Sklar remembered Mr. Rivera being warm and welcoming when she met him in 2012, while she was living in a shelter he ran on East 166th Street in the Bronx. His family also owned the building, and on occasion, he would swing by and tell her about his past struggles and his commitment to his Christian faith. They struck up a friendly rapport.

A few months into Ms. Sklar’s stay, Mr. Rivera offered to move her into an empty apartment in a building he owned in the Bronx, where he and his wife also lived. He told her that she would be safer there than in the shelter, and that a city program would cover her rent. Marveling at his generosity, she moved in early 2013, she said.

But once she was living in Mr. Rivera’s home, his tone shifted. He began flirting with her and grabbing her waist or trying to lift up her shirt, she said. Each time, she said, she tried to laugh it off and told him to behave himself. But she was growing increasingly alarmed.

One evening in December 2016, Ms. Sklar’s microwave began smoking and Mr. Rivera came by to help fix it, she said. Once inside her apartment, he asked to inspect the leaking ceiling in her bedroom, then shoved her against a wall and began touching her. As he pulled down his pants and demanded oral sex, he asked her if she liked living there.

“I felt like if I could just do it, I could keep my home,” she said. “I never felt so dirty or so disgusted in all my life.”

After he left, Ms. Sklar said, she peeled off her shirt that was soiled with his semen and saved it in a plastic bag — proof of the assault for the police. The Times spoke to two other women who rented rooms in Mr. Rivera’s home, Kenya White and Lillian Ortiz, who said Ms. Sklar had told them about the incident. Ms. White said she had repeatedly encouraged her friend to file a police report.

“She was too scared,” said Ms. White, who was Ms. Sklar’s roommate at the time. “He had her really petrified.”

Ms. Sklar told The Times she decided not to go to the police because she could not stomach the thought of revealing her private humiliation and was afraid that Mr. Rivera would evict her. But she said she ultimately agreed to share her story with The Times because she thought it would help her emotionally and she wanted Mr. Rivera to be held accountable.

In late 2017, another woman tried to sound an alarm about Mr. Rivera. After fleeing domestic violence that left her and her young children homeless, Marta Del Valle was living at a Bronx Parent Housing Network shelter where she encountered Mr. Rivera. She said he looked her up and down, asked if she was single and told her she “should try another guy,” which she understood to mean him. If she went along with his sexual advances, he implied, he could upgrade her room to one with a stove, which she wanted in order to cook for her four children.

“I was in shock,” Ms. Del Valle said. “I’m not here for that. I’m here to get an apartment.”

Ms. Del Valle immediately filed a complaint with the city’s 311 hotline, which alerted the Department of Social Services, according to a copy of her complaint reviewed by The Times. The department handed it off to the Bronx Parent Housing Network — where it was ultimately reported to Mr. Rivera, records show. Ms. Del Valle said staff members at the nonprofit interviewed her but seemed uninterested in pushing too hard. According to records, the internal investigation concluded that her complaint was unfounded because of a lack of evidence.

A spokesman for the Department of Social Services said the complaint “was not appropriately escalated to agency leadership” and should have been independently investigated.

The Times spoke to three other women who described similar encounters. One of them, Shaquana Graham, said she knew Mr. Rivera was making a sexual overture when she was in a shelter around the summer of 2017 and he ran his eyes over her body and slyly suggested they “hang out.” He continued to harass her, she said, but she tried to brush off the comments and keep her distance because she and her children needed a place to stay. “Men who have power feel like they can say and do what they want,” Ms. Graham said.

Maari Johnson was a young mother with a new baby and was staying in a shelter around 2010 when Mr. Rivera approached her for sex, according to Ms. Johnson and two of her caseworkers, who told The Times that she had informed them about the incident at the time. “He didn’t touch me, but he said things that were inappropriate,” Ms. Johnson said. Fearful of jeopardizing her housing, she asked her caseworkers not to complain.

Women who worked for Mr. Rivera also have contended with crude remarks, frequent sexual innuendoes and, in one case, assault, according to records and interviews with dozens of former staff members.

For a time, an employee at the nonprofit named Danielle Dawson was romantically involved with Mr. Rivera until she broke it off, according to a police report and interviews with her co-workers. On Dec. 22, 2016, after the relationship had ended, Mr. Rivera approached Ms. Dawson in a shelter where she worked and demanded they have sex, according to the report she filed with the New York Police Department.

When Ms. Dawson refused, Mr. Rivera slapped her in the face and said “Nobody tells Daddy no,” according to the report. Then he forced her to give him oral sex. Ms. Dawson was willing to press charges, the report said, but it was unclear whether the police ever investigated the incident further. Mr. Rivera was never criminally charged.

The police department declined to answer questions about the allegation, but said the “N.Y.P.D. takes sexual assault and rape cases extremely seriously.”

After the incident, Mr. Rivera fired Ms. Dawson, prompting her to file a complaint with the state for unlawful discrimination, according to public records and interviews with her colleagues. But in November 2017, the nonprofit paid her $45,000 not to pursue it further, according to a settlement agreement obtained by The Times. It included a provision that prevented her from talking publicly about what had happened, said Brian Younger, a shelter security guard in whom she confided at the time.

The next year, in 2018, Flora Montes, an administrative assistant at the Bronx Parent Housing Network, accused Mr. Rivera of sexual harassment and unwanted touching, according to a complaint she filed with the state and a draft of a lawsuit reviewed by Times. She said he repeatedly leered down her shirt, told her she was sexy and stroked her hair and back.

As Ms. Montes was preparing to file a lawsuit in 2019, the nonprofit paid her a $130,000 settlement that included a nondisparagement clause barring her from publicly discussing Mr. Rivera’s conduct, according to records reviewed by The Times.

The state Division of Human Rights, the agency that received complaints from both women, never alerted city officials to the allegations about Mr. Rivera. A spokesman for the division said it does not notify other agencies unless they are part of the complaint or have information to help with an investigation, and noted that both women had settled with no findings of guilt.

At the nonprofit, staff members openly discussed Mr. Rivera’s sexual aggression, with several likening him to Harvey Weinstein, the Hollywood producer who had been accused of assaulting women (and has since been convicted). One employee resigned in disgust.

“I can no longer continue to represent or be a part of this culture that has taken over our company,” Bernard Rodriguez, the former head of maintenance at one of the shelters, wrote in an email to the staff when he quit in 2018. “I am a father of a young girl would be devastated to know that she would be preyed upon by a predator that has leverage over her.”

The city had multiple warning signs of financial misconduct in Mr. Rivera’s organization, and confronted him at least three times about problems. While officials forced some changes, Mr. Rivera remained in charge and continued to find ways to enrich himself and his associates.

In early 2017, officials with the Department of Social Services called Mr. Rivera in for a meeting and told him to resolve a conflict of interest: He owned a for-profit housing company that shared staff and resources with the Bronx Parent Housing Network, according to three former employees.

That was not the only entanglement, The Times found.

The Bronx Parent Housing Network hired Mr. Rivera’s wife, brother and son-in-law, according to internal staff rosters and tax filings. His wife, who was promoted to a senior executive position at the nonprofit organization, was simultaneously working at the for-profit housing company that Mr. Rivera owned, according to a deposition she gave in an unrelated lawsuit.

Mr. Rivera also funneled women from his shelters into rooms in his Bronx home, allowing him to collect money the city pays to landlords who rent to homeless people. Three of the women who moved in told The Times the units Mr. Rivera rented to them were cramped, unventilated and filled with mold.

“We all trusted him,” said Mercedes Santiago, who moved there around 2017. “All he cared about was the money.”

Jennifer Redmond, a lawyer representing the Bronx Parent Housing Network, said Mr. Rivera had stepped down from his for-profit housing company and no longer collected a salary from it, and she denied that any staff members performed work on “B.P.H.N. time” at Mr. Rivera’s for-profit. She said Mr. Rivera’s family members had been hired based on their qualifications and that in the group’s early days, Mr. Rivera had relied on his family “to support his dream.”

Ms. Redmond said Mr. Rivera had disclosed to the city that he rented rooms in his house to homeless people, adding that he “works enormously hard to maintain the units properly.” The spokesman for the Department of Social Services disputed that, saying the city had not been told of the rentals.

A few months after the 2017 meeting between city officials and Mr. Rivera, a whistle-blower at the nonprofit complained to the Department of Social Services that Mr. Rivera’s nepotism and conflicts of interest had continued, according to a copy of the complaint.

In response, city officials again called him in to reprimand him and effectively instructed Mr. Rivera to end his wife’s employment at the nonprofit. She left the organization in late 2017.

In 2018, the city placed the Bronx Parent Housing Network on a corrective action plan, a special watch-list that meant the organization would be subject to increased scrutiny. Ten of New York’s approximately 70 shelter operators are under corrective action plans. All of them continue to receive city money.

City officials instructed Mr. Rivera to limit the hiring of other immediate family and said a lawyer had to review the group’s spending and contracts, especially any transactions with Mr. Rivera or his personal businesses.

Mr. Rivera agreed to comply, and city officials seemed satisfied that the organization was turning a corner. The Times, however, found that Mr. Rivera still sidestepped the mandates.

Soon after his wife left her executive role at the Bronx Parent Housing Network, she obtained a new job as vice president of the security company used by the nonprofit, according to internal emails and a meeting agenda obtained by The Times. The security company was paid more than $4 million by Mr. Rivera’s organization, according to city documents. (As The Times was asking questions about the security company, the city barred the nonprofit from contracting with the group.)

Ms. Rivera did not respond to multiple requests for comment, and Ms. Redmond, the lawyer, said Ms. Rivera had secured her new job “based upon her credentials.”

In another example of the chief executive’s mingling his personal and professional spheres, the nonprofit awarded $184,000 in maintenance contracts last year to a friend of Mr. Rivera’s who also performed work at a building he owns in the Bronx, according to city contracting records and an insurance certificate. Ms. Redmond, the lawyer, said Mr. Rivera did not recall whether he had informed the board of directors at the Bronx Parent Housing Network about the potential conflict.

Mr. Rivera’s organization also steered millions of dollars in rent to a company run by his onetime business partner, according to city and court documents. The Bronx Parent Housing Network has leased at least two shelter buildings — as recently as last year, records show — from a company called Urban Residences Corp., which is owned by Mr. Rivera’s former partner in a for-profit housing venture.

Through its lawyer, the Bronx Parent Housing Network said Mr. Rivera had no relationship to Urban Residences.

The Department of Social Services has defended its record in cracking down on the behavior of its shelter providers, including Mr. Rivera. The city, for instance, ended its contract with a Brooklyn nonprofit in 2017 after multiple news reports of financial problems and substandard shelter conditions, including a radiator explosion that killed two toddlers.

But the city has continued to work with other nonprofits that have shown signs of irregularities, including a major provider that in 2019 was found to have steered millions of dollars to a for-profit security company connected to top officials in the organization. The city referred the matter to investigators.

While The Times was reporting this story last year, the city confronted Mr. Rivera a third time about his financial connections. Still, it did not rescind any contracts.

In fact, this year is the best one yet for Mr. Rivera’s organization: The nonprofit has been awarded $91 million in city money.

As Mr. Rivera’s power has grown, Ms. Sklar has struggled to regain control of her life.

She said she plunged into a depression after the 2016 assault. She lived in fear that Mr. Rivera would barge into her room, so she slept with a knife tucked under her pillow and a chair propped against her door. She wanted to move out, but had no job, little money and few other housing prospects, she said.

Mr. Rivera continued to demand sex, she said, but she spurned his advances.

In retaliation, he moved her to a dank, moldy apartment on the ground floor, according to Ms. Sklar and her roommate. She lived in that unit until 2019, when at the urging of a friend, she moved out of Mr. Rivera’s home and tried to rid her thoughts of him.

But when she was watching a local news segment on television early last year, Mr. Rivera’s face appeared on the screen. His organization had just opened a new soup kitchen, and he was talking about his life’s mission to help those less fortunate. “I know what it is to be homeless,” he said, “and I know what it is to be judged in the greatest city in the world.”

Filled with rage, Ms. Sklar sat in silence.

Ali Watkins and Andrea Salcedo contributed reporting. Susan C. Beachy and Alain Delaquérière contributed research.