Five adult gray seals were found shot to death on Cape Cod beaches last month in what appears to be the most serious attack on marine mammals in at least three decades in New England.

The seals, all with gunshot wounds to the head, were found over a two-week period on beaches from Dennis to Chatham by the International Fund for Animal Welfare’s marine mammal rescue and research team. Investigators got their first clues to the gruesome deaths when they examined what they thought were two stranded seals and discovered bullet holes in their skulls.

They have subsequently identified three other seals killed in the same manner.

The shootings have occurred as gray seals — once hunted so widely that they all but vanished from Northeast waters — are making a dramatic comeback off New England, to mixed reviews.

While many beachgoers love to watch the 300- to 600-pound bulbous creatures frolic on beaches, the animals are believed to be luring great white sharks into coastal waters where people swim. And some fishermen complain the seals are depleting the fish population they depend on.

“I can’t think of another instance that gray seals and people are so close together . . . as Cape Cod,’’ said Jim Gilbert, a professor of wildlife ecology at the University of Maine who studies seals. “The closest you could come is sea lions and people’’ on the West Coast.

The National Oceanic and At mospheric Administration’s Office of Law Enforcement is investigating the deaths but released few details yesterday. Some seals may have been dead for several weeks. It is unclear if the animals died at sea or on the beach. More animals may have been shot at sea but not discovered.

Bullet fragments removed from the massive seals, as well as CT scans of their heads, are being analyzed, NOAA Special Agent Todd Nickerson said.

“I do worry if there will be more,’’ Nickerson said. “I don’t know, but it is certainly a concern to us.’’

Gray seals were once considered such marine pests that Maine and Massachusetts placed bounties on them. A seal nose and skin could fetch $5 in Massachusetts for much of the period between 1888 and 1962, according to a 2008 paper published in Northeastern Naturalist. An estimated 72,000 to 135,000 seals were killed in the two states as a result of the bounties, according to the paper.

But by 1972, the Marine Mammal Protection Act made it a crime to injure or harass seals. Violators can face up to $100,000 in penalties and a year in prison. Since then, seals have slowly been making a comeback off New England.

In the early 1980s, only a handful of gray seal pups were seen on Muskeget Island off the western tip of Nantucket, their prime breeding colony off Massachusetts. By 2008, 2,000 were seen there. Researchers don’t have a good handle on exactly how many gray seals are off New England now, but they suspect the population will level off once the animals fully repopulate.

The seals, which can grow to be 8 feet long, have created new haul-out, or resting, colonies on Cape Cod. People are not allowed to approach the colonies.

There have been few public conflicts between seals and humans in New England. Unlike the battles over unchecked populations of sea lions on the West Coast, there are popular seal-watching tours off Cape Cod, and beachgoers have cheered their comeback.

But that may be changing. Last year, a mature gray seal suffered massive head wounds from several gunshots and had to be euthanized in Truro. In 2007, a harp seal was found on Cape Cod with shotgun pellets in its head. And in 2004, a series of four suspicious seal deaths took place over a seven-month period, including a gray seal with its genitals cut out and a professionally skinned harbor seal that washed up on Hampton Beach in New Hampshire.

Sharp, of the animal-welfare fund, said she hopes the recent seal deaths are an anomaly.

“With the increase in the seal population, [people] are going to run into them more often,’’ Sharp said. “It is our responsibility to share our coastline. We should embrace them instead.’’

Anyone with information about the cases is urged to call NOAA law enforcement at 508-990-8752.

Beth Daley can be reached at b_daley@globe.com.

© Copyright 2011 Globe Newspaper Company.