Environmentalists are trying to establish how the whales beached on Rutland Island near Burtonport.
It's thought they were the same group spotted in the Outer Hebrides at the end of October.
Dr Simon Berrow of the Irish Whale and Dolphin Group said it was one of the biggest mass deaths of whales in Irish history.
He is concerned that Royal Navy sonar equipment could have played a role.
"Thirty or 40 pilot whales were spotted off the Outer Hebrides at South Uist last week," he said.
"It looked like they were going to strand. It was bad weather. They were not seen again."
Dr Berrow said the Royal Navy had been in the area off South Uist and had moved away.
Campaigners were concerned that the latest sonar equipment could have disturbed the navigational skills of this deep diving species of whales.
But a spokeswoman from the Royal Navy said that when the whales were spotted near South Uist, the closest navy ship was 50 miles away.
At that distance, she said, there was no way that the sonar equipment could have affected them.
In the past, the navy has denied that sonar noise from their warships could cause whales to beach.
However, in America, the US Navy was ordered not to use mid-frequency sonar during training exercises from 2007 and 2009, after a judge found in favour of campaigners who argued the devices harmed marine mammals in the area.
A team from Galway/Mayo Institute of Technology travelled to the scene off Donegal to take samples from the mammals.
Skin samples will also be sent to the Irish Cetacean Genetic Tissue Bank at the Natural History Museum in Dublin.
Sixty whales died in the 1960s off the west coast of Kerry and 35 to 40 animals died in north Kerry in 2001.
Eimear McGee: "They're a very strong social group... so the sick and the healthy died here together"
By Nuala McCann
BBC News
http://www.bbc.co.uk/news/uk-northern-ireland-11705622
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