Philippine authorities said Tuesday they have fined the US Navy for "unauthorised entry" after an American minesweeper went aground on a World Heritage-listed coral reef.

Manila announced the initial penalty amid growing anger in the Philippines over the January 17 stranding of the USS Guardian on the Tubbataha Reef, for which the US Navy has apologised.

A government-led board that manages the reef served formal notice Tuesday initially citing the US Navy for "unauthorised entry", Jose Lorenzo Tan, a member of the board, told AFP.

The site is protected by Philippine law, and is off-limits to navigation except for research or tourism approved by the marine park superintendent.

The law prescribes a maximum penalty of up to a year in prison plus a fine of up to 300,000 pesos (about $7,300) for unauthorised entry, but Tan said the penalty agreed by the board does not include the jail option.

"We initially decided to fine them," said Tan, also the country president of the World Wildlife Fund. He declined to disclose the amount.

A board statement issued by Tan said the US Navy would also be fined for "non-payment of conservation fee" and "obstruction of law enforcement officer".

The Tubbataha marine park superintendent, Angelique Songco, said Monday that park rangers had warned the USS Guardian by radio that it was nearing the reef, but the ship captain insisted they raise their complaint with the US embassy.

Fines for "damages to the reef" and "destroying resources" would be assessed after the vessel is retrieved, the board added.

The US embassy declined comment on the alleged violations.

Tubbataha is a UNESCO World Heritage Site on the Sulu Sea about 130 kilometres (80 miles) off the western island of Palawan.

The commander of the US Navy's 7th Fleet, Vice Admiral Scott Swift, apologised for the incident in a statement from Japan on Sunday.

The US Navy said the 68-metre (224-foot) vessel, which remained stranded above the reef Tuesday, had been en route to Indonesia after visiting a Philippine port north of Manila when the accident happened.