Philippine President Benigno Aquino has welcomed the US Navy's apology for a minesweeper that went aground on a World Heritage-listed coral reef, but said they would not be exempt from penalties.

The priority was to remove the damaged USS Guardian from Tubbataha Reef even as an investigation was under way to determine why it strayed into the area, Aquino told reporters in Davos, Switzerland, according to transcripts released Sunday.

"We'd like to thank them for respecting our sovereignty and are very careful about our sensitivities," Aquino said of the apology last week by the US embassy and the US Navy.

"But that doesn't exempt them from having to comply with our laws," he said.

The 68-metre (224 foot) vessel has been stuck since January 17. Its hull has been punctured and is now flooded.

The US Navy last week raced to remove some 57,000 litres (15,000 US gallons) of fuel from the ship, while awaiting the arrival of two bigger crane ships to pluck the Guardian from the reef.

The incident has caused anger in the Philippines, a former American colony and ally in the Asia-Pacific.

While both the embassy and the head of the US Navy's Pacific fleet have apologised for the incident, they have not yet explained the exact cause.

The head of the marine park supervising Tubbataha has said the ship ignored warnings that it was entering a protected marine sanctuary.

The government last week said it was seeking heavy fines for the coral damage, but Aquino said penalties would have to be assessed after the vessel is salvaged.

About 1,000 square metres (3,280 square feet) of coral has been impacted, or about less than one percent of the entire marine park.

Tubbataha is 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.

Under Philippine law, the sanctuary is off-limits to ships except for research or tourism vessels approved by the government. "They violated it, there are penalties," Aquino stressed.