Most of the sailors injured in a massive fire aboard the amphibious assault ship Bonhomme Richard Sunday suffered from smoke inhalation, Rear Adm. Philip Sobeck, commander of Expeditionary Strike Group 3, told reporters Sunday evening in San Diego, where the ship had been burning for nearly 12 hours.

The sailors were in stable condition, he said.

“Most of them are attributed to smoke inhalation,” Sobeck said. “I don’t have the facts of all of them.”

Seventeen sailors and four civilians were injured in the blaze.

While the precise cause remained unknown Sunday night, Sobeck said there was “nothing toxic” in the ship, and that the black smoke billowing from the amphib all day was caused by office and berthing items burning.

The fire is believed to have started below those spaces, in the lower cargo hold of the ship, known as the “Deep V,” Sobeck said.

It is a “huge open area where you store a lot of (Marine Corps) equipment and everything else,” he said. “That’s where we believe it was started.”

Bonhomme Richard had 1 million gallons of fuel onboard but it is “well below where any heat source is,” Sobeck said.

Sobeck noted that some sort of internal explosion had occurred earlier in the day aboard the ship, but said that “what we cannot ascertain is what that explosion was caused from.”

The explosion may have been a backdraft, he said, which occurs during a fire when oxygen rapidly floods an oxygen-depleted environment.

Sobeck said firefighters were onboard the ship battling the blaze as he spoke.

The remainder of the Bonhomme Richard’s crew was safely evacuated and accounted for, he said.

At about 5:20 p.m. local time Sunday, Naval Base San Diego’s official Twitter account ordered non-first responders to “shelter in place” in sector A, wet side, north of pier 5.

Naval Surface Forces spokeswoman Lt. Cmdr. Patricia Kreuzberger said the shelter-in-place order was not in response to any specific threat and was intended to keep the area cleared as first responders battle the fire.

In addition to an ashore safety perimeter, maritime traffic in the area was being kept away as well, officials said.

There were about 160 sailors on board the ship at the time of the fire. About 1,000 sailors are assigned to Bonhomme Richard, though on weekends a small duty section is in charge of running security and overseeing contractors.

Pictures of the ship circulating online show smoke billowing out of the decks and firefighters spraying the ship’s hull with water to cool the steel.

According to the local emergency scanner, officials were clearing the pier after “a large explosion” on the ship.

All ships on the waterfront have been told to provide fire parties in case they are needed to assist in the effort, SURFPAC said.

The ship was in the middle of a maintenance period that included upgrades to the flight deck.

At the time of the fire, the destroyers Russell and Fitzgerald were both on the same pier. The ships have been moved away for their safety, SURFPAC said in a statement.

San Diego Fire Chief Colin Stowell told CNN Sunday that the fire could burn for days “down to the water line.”

While what caused the fire and when it will be extinguished remained unclear Sunday night, the inferno aboard the 23-year-old ship risks becoming a so-called “constructive total loss” if the fire is allowed to burn itself out, according to Lawrence Brennan, a retired Navy captain who now teaches admiralty law at Fordham University’s School of Law.

“This could cost the U.S. Navy an important aviation asset, capable of handling modern F-35s,” he said in an email. “Repair prices, if practical, will be hundreds of millions of dollars, or replacement will take many years and cost about a billion dollars.”

— The Associated Press contributed to this report.

David B. Larter was the naval warfare reporter for Defense News.

Geoff is the editor of Navy Times, but he still loves writing stories. He covered Iraq and Afghanistan extensively and was a reporter at the Chicago Tribune. He welcomes any and all kinds of tips at geoffz@militarytimes.com.

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