The USS Guardian will be cut up and its pieces carried away from Tubbataha Reef on which the ship grounded on Jan. 17, Stars and Stripes reported Thursday.
Since the grounding, the hull of the ship has been breached by wave action rocking it against the reef, which was also damaged by the ship.
The Guardian will be disassembled from the top down, Navy spokesman Lt. Frederick Martin said in an e-mail.
Equipment on the deck will be removed first, followed by the masts and funnels. Sections of the superstructure will be cut apart, enabling heavy machinery inside to be removed. Finally the hull of the 224-foot vessel will be cut into three pieces.
Hazardous materials and fuel have already been removed.
Biologists will be able to assess damage to the World Heritage Site reef once cranes lift away the last pieces.
The extent and nature of possible restorations to the reef will be decided by weather and the reef's condition, said Walter Jaap, a coral reef ecologist.
Tubbataha is in an area of strong waves, which is a difficult place to work, he said.
"In a case such as this with catastrophic impacts it would be decades or more for resources to recover to pre-incident status," Jaap said.