Defense analyst Loren Thompson says he'll be surprised if the sub is returned to service.
Authorities say they are waiting for the sub to cool enough for fresh air to be safely introduced without risk of another fire.
Firefighters spent Wednesday night and early Thursday fighting the fire on the USS Miami in Kittery. Seven firefighters and crew members were hurt, but not badly.
The flames were isolated from the nuclear propulsion spaces but caused extensive damage elsewhere.
Rear Adm. Richard Breckenridge on Thursday called the firefighters heroes for saving the ship.
THIS IS A BREAKING NEWS UPDATE. Check back soon for further information. AP's earlier story is below.
Officials vented smoke and noxious fumes from a nuclear-powered submarine at a Maine shipyard Thursday so they could get inside to assess damage from a fire that took hours to put out.
Firefighters from the shipyard and coastal departments in Maine and New Hampshire spent Wednesday night and early Thursday fighting the fire on the USS Miami. Seven firefighters and crew members were hurt, but not badly. The cause of the fire is not yet known.
Rear Adm. Richard Breckenridge, commander of Submarine Group Two, said firefighters isolated the flames so they would not spread to nuclear propulsion spaces. There was nuclear fuel on board the sub, but the reactor has been shut down for two months and was unaffected.
The firefighters battled intense heat, smoke and noxious fumes in cramped spaces, Breckenridge said.
"There are a lot of heroes that worked together to save the ship," he said.
Crews responded at about 5:40 p.m. Wednesday to the USS Miami, which was in dry dock at the Portsmouth Naval Shipyard on an island in Kittery, near Portsmouth, N.H. It was not clear how many people were aboard at the time. The submarine is in the third month of a 20-month maintenance period.
Breckenridge said the fire started in the four forward compartments, which include living and command and control spaces.
No weapons were on board.
The USS Miami has a crew of 13 and 120 enlisted personnel. It arrived at the shipyard on March 1 to undergo maintenance work. It was commissioned in 1990 and its home port is Groton, Conn.