The seals were found by a group of veterinary students near Beach Point.
The 10 grey seal pups examined so far had severely fractured skulls, said Pierre-Yves Daoust, a wildlife pathologist at Charlottetown's Atlantic Veterinary College.
Radiological images were taken of eight of the pups and none showed metal fragments, indicating they were not shot.
Daoust said he has not seen large numbers of dead seals like this before, and he and fisheries officers were suspicious from the start that the seals were killed by people.
"It is a black eye … to Prince Edward Island, and to the Maritimes," said Daoust.
The necropsy showed that not all the animals were killed instantly by their injuries, and that all were left to freeze.
"This cannot be done. This is not acceptable. This has nothing to do with the seal hunt. That is not what a professional sealer would do," said Daoust.
"A professional sealer would make sure that the animal is used as much as possible [and] would make sure that the animal dies as quickly as possible. When we see something like this, which is totally the opposite, … it gives such a poor image."
An incident such as this affects the whole industry, he said.
Officials from the Department of Fisheries and Oceans are investigating.