WASHINGTON — The federal government is deliberating over a proposal to protect the coastal waters that are home to the northern right whale, which has been hunted to the brink of extinction and is the most endangered of the large whales.

A scientific advisory panel, made up of whale experts from inside and outside the government, has formally petitioned the National Marine Fisheries Service to designate two areas off Massachusetts and one stretch along the Georgia-Florida shore to be `critical habitat’ for the 45-foot, black whales.

“Designation of critical habitat is one of the most important actions that The United States government can take to protect the northern right whale,” Hans Neuhauser, chairman of the Right Whale Recovery Team, wrote to the fisheries service.

Researchers estimate there are about 350 of the endangered whales in the western North Atlantic and another 300 in the northern Pacific.

The panel petitioned the agency to designate as critical most of Cape Cod Bay; the Great South Channel, an offshore area east of Cape Cod and Nantucket; and a 15-mile wide strip of coastline from the Altamaha River in Georgia to Jacksonville, Fla., that then narrows to five miles wide south to Sebastian Inlet, Fla. The whales, which range north into Canada, spend early spring feeding off Massachusetts, and females give birth in the southern waters during the winter.

If the service approves the plan, it would be the first time the U.S. government has designated a critical habitat for any of the seven endangered large whales, according to agency officials.

“In spite of the fact that they’ve been protected for more than 50 years from hunting, we don’t know yet whether the population (of northern right whales) is increasing, decreasing or staying the same,” Neuhauser, a vice president of the Georgia Conservancy, said in a telephone interview. “If it is increasing, it’s doing so very slowly.”

The panel listed four main threats to the marine mammals: collisions with ships; entanglement in fishing nets and gear; municipal sewage, industrial runoff, oil spills and other pollution; and disturbance by whale-watching vessels.

The designation would be the first step in implementing a broader draft recovery plan finished in February, but it is not clear how the ruling would affect shipping, fishing and other activities along the Eastern Seaboard.

“What critical habitat designation does is it says if a federal agency wants to do something either in that area or that would affect that area, they have to consider the impact on the right whale habitat, not just on the right whale itself,” said Neuhauser.

The ruling, for example, could affect the U.S. Army Corps of Engineers, which issues permits for the ocean dumping of dredge waste, or states seeking permits to discharge sewage into the sea. It might also force ship captains to post whale lookouts or slow down as they pass through designated critical habitat.

“By designating critical habitat, it heightens awareness that this habitat is essential for this species, and all of the benefits that accrue from that will hopefully help,” said Doug Inkley, a wildlife ecologist with the National Wildlife Federation.

But some elements in the recommendation could provoke opposition. The Great South Channel site, for instance, encompasses a section of the major shipping lane between Boston and New York City. And the southern habitat includes the passage used by U.S. Navy Trident submarines heading out to sea from their King’s Bay base in Georgia.

“So far the Navy has been surprisingly cooperative in this effort,” noted Neuhauser, who said that panel members are also establishing contact with shipping concerns along the coast.

The fisheries service is accepting public comments on the proposal until Sept. 10, but the agency has up to a year to make its ruling, according to Robert C. Ziobro, a fishery biologist with the agency.

Whatever the agency’s decision, whale experts do not expect the northern right whale to make a quick resurgence.

“The recovery of the right whale will take a great number of years, and won’t be seen in our lifetimes,” predicted Ziobro.