About 60 grey seals have been culled on one of the Blasket Islands off the coast of Co Kerry.
The Irish Seal Sanctuary blamed local fishermen for the slaughter of the seals.
"There's only one direction the finger can be pointed at: the fishing community," said group spokesman Mr Sean Eviston, who travelled to Beginish Island off the coast of the Dingle peninsula to confirm reports of the cull.
Mr Eviston said the grey seals killed were mostly "whitecoats," pups about three weeks old. He said the attackers appeared to have used several methods to kill, including gun shots, beating the animals with rocks, and driving nails into their skulls.
"They ripped some of these seals open from the nape of the neck," he said.
Gardaí are investigating.
The Minister for the Environment, Mr Dick Roche, described the slaughter of the seals as "cruel and barbaric". He has sent a department official to the islands to investigate.
"The cruel and barbaric slaughter of these seals has a de-humanising effect on society. The sight of seals being bludgeoned to death is repugnant," mr Roche said.
Fishermen have been blamed for occasional slaughters of seals on the islands that dot the western and southern coasts of Ireland. Nobody has ever faced charges.
Grey seals are supposed to be a protected species under Ireland's Wildlife Act of 1976. Beginish is part of the Blasket Islands, Ireland's largest sanctuary for grey seals. The Irish Seal Sanctuary estimates that fewer than 400 grey seals are resident in the islands, down from about 2,000 a half-century ago.