The Philippines has ordered the US navy to pay $1.5 million in compensation for the damage to a world heritage-listed coral reef caused by an American warship.

An assessment by Philippines authorities estimates 2,400 metres of the Tubbataha reef was damaged when the US minesweeper ran aground in January.

The area affected is less than earlier estimated, but the Philippines has issued a damages claim of $1.5 million.

In a statement, the Tubbataha Management Office said the fine was "but a slap on the wrist" compared to the $45 million spent on salvage operations.

Washington has assured Manila it will pay for the damage to the reef and help in its recovery.

It has also stood down the commanding officer and three crew from the ship, which was removed from the reef in pieces to avoid further damage.