The double-crested cormorant may be legally protected, but if the town of Chilmark and the Wampanoag Tribe of Gay Head (Aquinnah) get their way, the Island will soon see fewer of the pesky birds, whose voracious appetites threaten fish restoration projects.

The tribe is seeking a special permit from the U.S. Fish and Wildlife Service to harass and kill the birds in order to protect the historic herring run. Chilmark is applying for the same permit to protect the new flounder restoration project. This is the first time the town has applied for the permit.

Federal, state and local laws protect the animal, known as a species of critical concern, and a special permit is needed to harass or kill them.

Bret Stearns, director of the natural resources department for the tribe, said he estimates the birds in the creek number in the hundreds. Per the guidelines of the permit, the tribe would be allowed to kill 10 per cent of the total estimated bird population, but can use non-lethal means to harass all of them with the goal of protecting young herring.

The tribe would use pyrotechnics such as bangers, a shotgun shell with no ballistics, to scare birds from the run, and would likely use a shotgun with non-lead bullets to kill the allotted amount of birds, he said.

“What you’re hoping for, really, is in the process of harassing them and getting them off where you don’t want them to be, and taking a few of them, they don’t come back to that location,” Mr. Stearns said.

Cormorants eat between three to five fish in one sitting, said Mr. Sterns. “They’re unbelievably gluttonous.”

Cormorants have been an ongoing issue for fishermen and tribal members. In 2003, tribal members William (Buddy) Vanderhoop Jr. and his brother Brian (Chip) Vanderhoop shotgunned 11 cormorants after becoming annoyed by the cormorants feasting on the fish. Aquinnah police, state environmental police and tribal council became involved.

Mr. Stearns said the permit will allow him to target birds only in the herring run. Chilmark must apply for their own permit and Aquinnah could do so as well.

The Chilmark selectmen unanimously voted to apply for the permit at their weekly meeting last Tuesday.

Selectman Warren Doty said the flounder restoration program, a joint effort between the tribe and the Martha’s Vineyard/Dukes County Fishermen’s Association to raise winter flounder, would benefit from the depredation permit.

“Releasing all these small fish into the pond, I know cormorants love to eat them,” said Mr. Doty. “We want to reduce their population so the flounder resource can revive.”

“As well as the herring,” selectman Jonathan Mayhew added.

Chilmark shellfish constable Isaiah Scheffer this week said he thought the permit was “a great idea.” Mr. Scheffer estimated there are at least 50 to 100 birds in each of the town ponds — Squibnocket, Quitsa, Chilmark and Menemsha — as well in the harbor.

“Just being on the water every day I personally can see it happening; they’re really proficient predators,” he said. “Almost every time they go down they come back up with something. I think the permit itself is great in theory, but it’s going to take somebody going out there and following through with it.”