US Edition Villagers waded chest deep into the water, clapping their hands and splashing to drive the mammals away while a flotilla of fishing boats guided them to open water.
"It's something unusual," said Malcolm Sarmiento, director of the Bureau of Fisheries and Aquatic Resources. "It's the first time that such a large pod has entered Manila Bay, and is acting strangely."
When they were spotted, the confused dolphins were swimming back and forth between Pilar and Orion townships in Bataan province about a mile off shore.
Mr Sarmiento told local radio that the dolphins may have become disorientated by a "heat wave or disturbance at sea" such as a possible underwater earthquake which could have damaged their eardrums.
"If their eardrums are damaged they become disorientated and they float up to the surface," he said.
Alternatively, he suggested, they could have followed a sick or injured leader. In that case, experts say, the leader must be identified and removed from the pod to prevent it from leading the others into danger again.
The pod included 200-300 dolphins but only three died. It is common for dolphins to beach themselves in the Philippines but rarely in such great numbers. On this occasion they were melon-head dolphins which are considered a "threatened species", meaning they are likely to become endangered in the future.