MANILA, Philippines >> Workers in the southwestern Philippines have removed the last major part of a U.S. Navy minesweeper from a protected coral reef where it ran aground in January, and the damage will be assessed to determine the fine Washington will pay, officials said Sunday.

A crane lifted the 250-ton stern of the dismantled USS Guardian on Saturday from the reef, where it accidentally got stuck Jan. 17, officials said. The reef, designated a World Heritage site by UNESCO, the United Nations’ cultural arm, is located in the Tubbataha National Marine Park in the Sulu Sea, about 400 miles southwest of Manila.

The doomed ship’s parts will be transported to a Navy facility in Sasebo, Japan, to determine which ones can be reused and which will be junked, Philippine coast guard Commodore Enrico Efren Evangelista said.

Workers were cleaning debris at the site, where American and Filipino experts this week will begin a final assessment of the reef damage, to be paid for by Washington. An initial estimate showed about 4,780 square yards of coral reef was damaged by the ship grounding, according to Tubbataha park superintendent Angelique Songco. She said it was unlikely the estimate would change significantly.

Songco said the fine would be about $600 per square meter, so the U.S. could be facing a bill of more than $2 million.

The fine will go to a fund for the upkeep of the reef, Songco said, adding that Filipino and U.S. scientists will inspect the reef this week to determine the best way to “rehabilitate” the damaged parts. One option is to let the reef heal by itself, which would take a long time but be less complicated. Another option is to carry out some “repairs” to the reef, which would be more costly and complicated, she said.

Songco said her agency did not have plans to pursue charges against U.S. authorities over the incident.

Asked if the Philippine government would press charges against U.S. Navy officials, Philippine Secretary Herminio Coloma Jr., a spokesman for President Benigno Aquino III, did not reply directly, but said, “There must be accountability and we will enforce our existing laws.”

The warship’s removal closes an embarrassing episode as Washington reasserts its presence in Asia amid China’s rise. The Navy and the U.S. ambassador to Manila, Harry K. Thomas, have both apologized for the grounding and promised to cooperate with America’s longtime Asian ally.

“As we have stated in the past, we regret this incident and the United States is prepared to pay compensation for the damage to the reef,” the U.S. Embassy said in a statement, adding that it was cooperating with a Philippine government investigation of the incident.

A separate U.S. government investigation on the cause of the grounding has not yet been completed, the embassy said.

Aquino has said that the U.S. Navy must explain how the ship got off course, and that the Navy will face fines for damaging the environment.

The Guardian was en route to Indonesia after making a rest and refueling stop in Subic Bay, a former American naval base west of Manila, when it ran aground before dawn Jan. 17. It strayed more than 3 miles into an offshore area off-limits to navigation before hitting the reef, Songco said.

Philippine officials are considering asking the International Maritime Organization, the U.N. agency responsible for improving maritime safety, to declare the Tubbataha park a “particularly sensitive sea area” so steps can be taken to further protect the area from future shipping accidents, she said.