No one aboard the USS Guardian was injured when the vessel hit the Tubbataha Reef about 2:25 a.m. local time, the Stars and Stripes reported.
The 224-foot Avenger-class mine countermeasures ship has a crew of 80.
A Navy spokesman said attempts were being made to free the ship, which was stuck about 80 miles east-southeast of Palawan Island. Information about damage to the vessel was not immediately available.
The Guardian, based at Sasebo Naval Base in Japan, was crossing the Sulu Sea between the southwest Philippines and Malaysia after a port visit to Subic Bay, the statement said.
The Philippine government has been notified of the incident.