Angelique Songco, head of the government's Protected Area Management Board, said the government imposes a fine of about $300 per square meter (yard) of damaged coral, plus other fees.
In 2005, the environmental group Greenpeace was fined almost $7,000 after its flagship struck a reef in the same area.
Songco blamed the Guardian for turning away park rangers who wanted to board the minesweeper, but the Navy said it was cooperating with the Philippine government, a key U.S. defense ally.
Presidential spokeswoman Abigail Valte said the government will observe the law governing the Tubbataha Reef, but right now "the primary concern is extricating the ship out of the reef with minimal damage."
Associated Press writer Audrey McAvoy in Honolulu, Hawaii, contributed to this report.