Salvage teams have begun cutting up a US Navy ship stranded on a UN World Heritage-listed coral reef in the Philippines in a process that could take almost month, the coastguard said on Wednesday.

The smokestack, or funnel, of the minesweeper USS Guardian was lifted off on Tuesday while the mast was removed on Wednesday, marking a major step in the operation, said coastguard spokeswoman Lieutenant Greanata Jude.

The 68-metre (223-foot) vessel ran aground on the Tubbataha Reef in a remote part of the Sulu Sea on January 17 and strong winds and heavy seas have hampered the operation to dismantle it.

The United States has repeatedly apologised for the incident, which it has blamed on faulty maps, but the incident has fuelled anger in the Philippines, a former American colony and important US ally in the Asia-Pacific region.

"Most of the equipment on top of the deck has already been transferred to a barge but they have yet to remove the large equipment inside the ship," Jude told AFP.

The dismantling of the ship has been repeatedly delayed by bad weather, but clear skies are now forecast to last over the next few days, she added.

The US Navy had originally targeted March 23 for the full removal of the vessel but the recent bad weather could now change the timeframe, Jude said without giving details.

Jude said the team has also removed a winch used to operate the vessel's sonar equipment, and are preparing to take apart the second level of the ship, located beneath the deck.

Sensitive equipment will be recycled but most of the ship will have to be scrapped after its fibreglass-reinforced wooden hull was breached when it ran aground, she said.

Portable equipment as well as toxic substances have already been removed from the ship, she added.

When it ran aground, the ship damaged a section of reef, a UNESCO World Heritage site, known for its rich marine life. President Benigno Aquino has said the US Navy will have to pay penalties for the damage.

The vessel, estimated to cost about $277 million, was too badly damaged to be towed away, the US Navy said earlier.

Vessels sailing into the Tubbataha 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 that it was about to hit the reef.