At least 18 US sailors have been taken to hospital after being injured in a large blaze on board a military ship at San Diego.

Naval Surface Forces said about 160 sailors were on board the 250-metre USS Bonhomme Richard when the fire was reported about 8.30am Sunday (local time).

Firefighters arrived at the San Diego Naval base to find thick black smoke billowing hundreds of metres into the air from several points along the amphibious assault ship.

Emergency crews fought the fire from boats alongside the burning ship.

“18 sailors have been transferred to a local hospital with non-life threatening injuries,” Naval Surface Forces wrote on Twitter on Sunday.

“The entire crew is off the ship and all are accounted (for).”

Tweet from @SDFD

The fire, which erupted just as sailors were leaving the ship, could potentially burn for days and down to the water line, San Diego Fire Chief Colin Stowell said.

“The navy is the only one that will work from the pier side, as well as the harbor PD on the fire boats, working from the water side to contain the heat of it,” Mr Stowell told CNN.

Three fire alarms alerted emergency services to the blaze between 9am-10am. Initial reports indicated the fire had started in the wall deck, where small landing craft enter and exit the ship.

The San Diego Fire-Rescue department wrote on Twitter that there had been an explosion at the ship and it was working to clear the area.