Firefighters responded to Pier 70 after fire and smoke was reported on the U.S. Naval Ship Henry J. Kaiser at about 9:40 a.m., fire spokeswoman Mindy Talmadge said.
Pier 70 is the site of one of the largest ship repair yards on the West Coast, according to its website.
Talmadge said crews repairing the ship had been working on an empty below-deck diesel tank when they noticed fire and smoke.
She said the fire may have been a burning thermal layer, a protective blanket that is used with equipment such as blowtorches.
Reaching the fire proved difficult, Talmadge said, because there was a single point of entry and egress into the tank, which she said is about 75 feet deep.
"We're going in to confirm and make sure everything is out," she said.
No injuries were reported.
The Coast Guard assisted in the response and said it dispatched a small boat to the area from Sector San Francisco, which is on Yerba Buena Island.