As darkness fell, local officials in Hokota, 60 miles northeast of Tokyo, said they had been able to save only three of the 149 animals that had beached and that the rescue effort had been called off.
The rest of the creatures, a member of the dolphin family usually found in the deep ocean, had either died or were dying, they said.
"It was becoming dark and too dangerous to continue the rescue work at this beach, where we could not bring heavy equipment," said an unnamed Hokota city official.
"Only three of them have been successfully returned to the sea, as far as we can confirm," he added.
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Locals and coastguard teams had battled through the day to save the animals, trying to stop their skin from drying out as they lay on the sand.
Others were carried in slings back towards the ocean.
Television footage showed several animals from the large pod had been badly cut, and many had deep gashes to their skin.
An AFP journalist at the scene said that some of the creatures were being pushed back onto the beach by the tide soon after being released, despite efforts to return them to the water.
While the reason for the beaching was unclear, Tadasu Yamadao, a researcher at the National Museum of Nature and Science, said the dolphins might have got lost.
"Sonar waves the dolphins emit might have been absorbed in the shoals, which could cause them to lose their sense of direction," he told the Yomiuri Shimbun.
In 2011, about 50 melon-headed whales beached themselves in a similar area.
Today's rescue effort stood in marked contrast to the global view of Japan and its relationship with cetaceans.
It has never made any secret of the fact that meat from the animals is consumed.
A UN court ruled last year that its hunt was a commercial activity masquerading as research and ordered it be halted.