A badly damaged minesweeper stranded on a World Heritage-listed coral reef in the Philippines for nearly two weeks will need to be dismantled before it is removed, the US Navy said Wednesday.

The drastic measure of pulling apart the 68-metre (224-foot) USS Guardian was proposed in a salvage plan to Philippine authorities, navy spokesman Lieutenant Commander James Stockman said in a statement.

"The US Navy has presented a salvage plan... that involves the dismantling of the ship. This was determined to be the best option and would involve the least damage to the Tubbataha Reef," he said.

The Guardian became grounded on the Tubbataha Reef, a UNESCO World Heritage Site in a remote part of the Sulu Sea, on January 17.

The US Navy had previously said the boat, which has a wood and fibreglass hull, was too badly damaged to be towed away, but had not come up with a firm alternative plan as to how it would move the vessel off the reef.

Thousands of litres of oil on board the Guardian have been removed but the vessel is being battered by huge waves, causing it to gouge a destructive trail along the reef, according to superintendent of the Tubbataha marine park Angelique Songco.

She said dismantling the ship would further damage the reef but letting it remain there longer would lead to even more harm.

"It will cause more damage the longer it is left there," she said.

The head of the Philippine office of the World Wildlife Fund, Jose Maria Lorenzo Tan, agreed the ship should be dismantled if there was no other way to shift it off the reef.

"If this is the only option, then the sooner they can remove it, the better. They cannot risk that the ship simply break apart," he said.

The US Navy has repeatedly apologised for the incident but has refused to explain publicly why the Guardian was sailing so close to the reef.

This has fuelled anger over the incident in the Philippines, a former American colony and important US ally in the Asia-Pacific region.

Vessels sailing into the marine park need permission, but Philippine authorities said the crew of the Guardian had made no request to enter and had even ignored radio messages from government rangers that it was about to hit the reef.