The assessment, conducted by the U.S. Navy itself, was rejected because Philippine officials were not allowed to inspect the damaged section of the reef themselves, Stars and Stripes reported Tuesday.
The Navy broke a previous agreement by excluding members of the Tubbataha Protected Area Management Board from a 10-day assessment of the reef by a Navy biologist and prohibited the board from inspecting the area themselves, said park administrator Angelique Songco.
Philippine Coast Guard officials said they were not aware an assessment had been conducted.
Since grounding on Jan. 17, the USS Guardian has slid around the reef, damaging the World Heritage site and causing breaches to the ship's hull.
Navy officials announced last week the ship, based at Sasebo Naval Base in Japan, was a complete loss and would have to be cut up to be removed from the reef. That process is expected to take a month.
The U.S. government has repeatedly apologized for the accident and has offered compensation in several forms including a $100,000 to a Philippine university to aid in coral restoration research at the reef and funding efforts to improve cartographic information on the reef.