Thirty-two of the short-finned pilot whales came ashore during high tide early yesterday in Probolinggo, East Java province.
"At first there were just one or two whales swimming near the shore, and the nature of whales is that if they are sick they will come near the shore," Dedy Isfandi, the head of the local maritime and fisheries office, told AFP.
"But whales have such high social interaction -- when one fell ill, they approach the sick one to swim back to sea... when the tide fell all of them were trapped," Isfandi added.
About 23 others were already out at sea while one disoriented whale was accompanied by some rescuers to make sure it did not return to shore.
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Rescuers used tarps to wrap around the beached sea mammals and pull them out to sea while swimmers plunged into the water to drive others out of the area.
Vets and scientists conducted autopsies on the dead whales to find out why they were stranded, but fishery officials said it could be due to turbulent waters in the Indian Ocean or they had eaten something poisonous.
Conservation group International Union for Conservation of Nature said there was insufficient data to classify the risk of extinction of short-finned pilot whales, which are found in warm temperate to tropical waters.