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.