The US Navy said Thursday it needed to remove thousands of litres of oil from a minesweeper stuck on World Heritage-listed coral in the Philippines, warning it was too badly damaged to be towed away.

The 68-metre (224-foot) USS Guardian, which became embedded in the Tubbataha Reef a week ago, will have to be lifted onto another ship or barge, a process that might take another fortnight, Rear Admiral Thomas Carney said.

"The option that we hoped to be able to tow the ship off the reef is not available," said Carney, who heads the US Navy's logistics group in the western Pacific.

"It's too badly damaged. It's got hull penetrations in several places, and there's a significant amount of water inside the ship right now."

He said the Guardian had listed after being battered by huge waves, and the most pressing issue was to remove 57,000 litres (15,000 US gallons) of fuel.

"The first priority is to get the fuel out of the ship as soon as possible," Carney told reporters.

Carney described the salvage operation as "a very deliberate, complicated process" involving at least two more US Navy vessels that could take up to two weeks to complete.

"It depends on the environmental conditions out there as to how safely we can proceed," he said of the timeline.

While Carney said it was too early to determine how much damage the Guardian has caused, the Philippine government reported this week that about 1,000 square metres (3,280 square feet) of coral had already been impacted.

This equates out to roughly one percent of Tubbataha, a UNESCO World Heritage site in a remote part of the Sulu Sea famous for its rich marine life and coral that rival Australia's Great Barrier Reef.

The incident has stoked anger in the Philippines, with the US Navy yet to explain why it was sailing through a protected marine sanctuary en route to Indonesia.

The head of the agency supervising the sanctuary said this week that the captain of the ship ignored warnings that it was nearing the reef. The agency recommended the US Navy be fined for "unauthorised entry" into the area.

Carney declined to explain why the Guardian was sailing in the area, saying that was still the subject of investigation, however he repeated a US Navy apology made last weekend.

"We express our deepest regret that we are in this situation, and we are committed to removing the ship from the reef as soon as possible," he said.