The Scottish SPCA is appealing for information about the deaths of the six common seals, discovered by Scottish Natural Heritage workers.
SPCA inspector Ron Patterson attended the scene at Mara Ness, Bridge of Walls, Shetland, on June 7.
He said three of the animals had clear exit wounds to the head and three were too decomposed to determine the cause of death.
Post-mortem tests showed that two female seals were carrying large pups.
The charity said it believes the six seals were shot and that more seal carcasses could wash up in other areas.
Mr Patterson said: "This is a serious wildlife crime and we are therefore very keen to speak to anyone who may have witnessed seals being shot in the area or who may have information relating to the shooting of seals.
"Common seal numbers are decreasing and the illegal shooting of seals is a contributing factor.
"In fact it's almost wrong to call these animals common seals because they are gradually becoming a rare sight in the waters around Shetland."
He said common seals are breeding and having pups this month.
Anyone with information should contact authorities.