There's also a chance the USS Guardian might break up or sink if crews tried to remove it without taking it apart first, U.S. Pacific Fleet spokesman Capt. Darryn James said.
Limiting damage to the coral, which is part of a national marine park, is important to the Navy, James said.
"We really do care about being good stewards of the environment," he said by telephone from Pacific Fleet headquarters in Pearl Harbor.
The Navy has presented the ship removal plan to the Philippines, which is reviewing it.
"We're working very closely with the Philippine coast guard, with their navy and their government personnel. We've been grateful for their support as we all work together to remove Guardian and minimize further damage to the reef," James said.
It's expected to take over a month to dismantle the Guardian, which ran aground before dawn on Jan. 17.
Crews have already removed 15,000 gallons of fuel from the ship. They've also taken off hundreds of gallons of lubricating oil and paint. They'll be removing human wastewater and other materials that could harm the environment, James said.
The U.S. Navy is hiring floating cranes to help with the removal. A contractor in Singapore is sending the cranes, which should arrive on site in a few days.
The Navy originally said the Guardian would be lifted by crane onto a barge and taken to a shipyard. But now the Navy says the ship is "beyond economical repair."
No one was injured when the ship ran aground at the reef in the Tubbataha National Marine Park. The park is a World Heritage Site in the Sulu Sea, about 400 miles southwest of Manila.
The Guardian was on its way to Indonesia after making a rest and refueling stop in Subic Bay, a former American naval base west of Manila.
Vice Adm. Scott Swift, the U.S. 7th Fleet Commander based in Yokosuka, Japan, has ordered an investigation into the grounding.
The incident damaged at least 1,000 square meters, or 1,200 square yards, of coral reef, according to an initial, conservative estimate by the Philippine coast guard.
Angelique Songco, park manager of Tubbataha Reef, the damage is the worst ever in the sanctuary since the park was established in 2001.
The Navy and the U.S. ambassador to the Philippines, Harry K. Thomas, have apologized for the grounding and promised to cooperate with its close ally.
Philippine President Benigno Aquino III said last week that the U.S. Navy must explain how the ship got off course. He said the Navy would face fines for damaging the environment.
The Navy paid the state of Hawaii $8.5 million to settle claims after a much larger vessel, the USS Port Royal guided missile cruiser, damaged thousands of square yards, or thousands of square meters, of coral when it ran aground off Pearl Harbor in 2009.
Reattaching more than 5,000 broken coral colonies and otherwise restoring that reef cost the Navy more than $6.5 million.
The Guardian is 224 feet long, less than half the length of the Port Royal.
The Navy last dismantled a grounded ship in 1971, after the USS Regulus ran into trouble when a typhoon lashed Hong Kong, James said.
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