This file photo shows USS Guardian warship, on January 22, 2013, sitting aground on the Tubbataha Reef in the Sulu Sea, Philippines, where it ran aground five days earlier. The Philippines will ask the US to pay $1.4 mln in compensation for damage caused by the ship to a protected coral reef, according to the manager of the reef.

The Philippines will ask the United States to pay 58 million pesos ($1.4 million) in compensation for damage caused by a US warship to a protected coral reef, the manager of the reef said Saturday.

The amount is based on studies by Philippine agencies including the coast guard that found the USS Guardian damaged at least 2,345 square metres (25,240 square feet) of the protected Tubbataha reef, park superintendent Angelique Songco said.

She said a letter requesting compensation would be sent to the US embassy next week, stressing this is the amount required by a law passed to protect the reef, a in a remote area of the Sulu Sea.

"We don't want to be dishonest. It is just a simple process: measure it correctly and then they pay. That is all. It is very straightforward," she told AFP.

Earlier estimates said as much as 4,000 square metres of the reef had been destroyed when the USS Guardian minesweeper ran aground on Tubbataha on January 17 but Songco said their studies found the damage was less than feared.

It took the salvage teams until March 29 to remove the last of the 223-foot (68-metre) USS Guardian, which had to be cut into pieces so it could be lifted clear without damaging the reef further.

The incident stirred nationalist anger with demands that the pay a large amount of compensation for damaging the reef, which is world renowned for its rich marine life.

But Songco said they would only ask for the required amount based on the affected area.

"I am not worried about criticism (for the small amount). We are not trying to put one over them and we hope they will do the same with us," she said.

She said the last of the salvage ships had left Tubbataha but a team of US Navy divers and a US vessel remained in the area, assessing the damage.

The United States has apologised for the mishap and has said it would cooperate in addressing the damage.

The US Navy said in a statement Saturday that it did not want to speculate about the liability but would coordinate with the Philippine government to assess the damage to the reef.

"The Republic of the Philippines may submit to the Navy any and all information it believes relevant to determinations of coral damage," the statement said.

The commanding officer and three crew of the USS Guardian were relieved of their duties over the grounding, the US Navy announced earlier this week.