The USS Guardian had been stuck on the Tubbataha Reef in the Sulu Sea since hitting it early Thursday, GMA News reported Friday.
All 79 members of the Guardian were transferred to two support vessels for safety reasons, the U.S. Navy's 7th Fleet said in a statement posted on its website.
"Several support vessels have arrived and all steps are being taken to minimize environmental effects while ensuring the crew's continued safety," Adm. Scott Swift, the 7th Fleet commander, said in the statement.
The reef is home to more than 1,000 species, many of which are endangered. It is a popular dive site and has been called one of the wonders of nature.
Speculation about damage to the reef would be "premature," said Lt. Brian Wierzbicki, 7th Fleet spokesman.
The Philippine Coast Guard said it would send a team to determine if the reef was damaged and if there was an oil spill.