The incident stirred nationalist anger against the United States, a former colonial ruler of the Philippines that remains the Southeast Asian nation’s most important military ally.
Washington promptly apologised for the mishap and issued a report five months later that blamed the captain and three other officers.
The vessel, which was en route to Indonesia after visiting a northern Philippine port, was found to have sailed into a protected area where marine vessels are not allowed due to “poor voyage planning”, according to a copy of the report.
In a statement on Wednesday, the Philippine foreign department said it received last month “the full requested amount” of 87 million pesos ($1.97 million) in compensation.
“The compensation will be utilised for the protection and rehabilitation of Tubbataha Reef Natural Park, a UNESCO World Heritage Site,” it said in a statement.
Part of the money will also be used to enhance monitoring activities in the area to prevent similar incidents in the future, it added.
The United States will also help the Philippine Coast Guard upgrade a patrol station guarding the reef, it said.
US embassy spokesman Kurt Hoyer confirmed to AFP that Washington had paid full compensation for the damage.
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