Residents of nearby Menia Village managed to save ten of the whales, all roughly three to four metres long, in a rescue attempt on Friday.
"There were some lacerations on their body from the contacts with rocks," local marine conservation agency head Ikram Sangaji told AFP.
He added that the injuries on the whales indicated they were not handled properly during the rescue.
Wildlife dept recovers protected animals
Six of the animals were buried in a traditional ceremony but one was chopped apart by some of the villagers for its meat, Sangaji said.
Local officials had taken samples of the bodies to investigate the deaths and why they were stranded.
Sangaji said in 2012 more than 40 whales were found stranded on the beach Kolo Udju beach on the coast of Menia Village, East Nusa Tenggara.
Cross-currents off the beach pose a danger to whales as they can easily get caught between the frigging reefs during the tidal waves, he said.
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