A US warship that ran aground on a protected coral reef in the Philippines was doomed by its top officers' "lack of leadership", the US Navy has concluded in a report released Friday.

The minesweeper USS Guardian became stranded on top of the Tubbataha Reef in the southern Philippines before dawn on January 17 and had to be cut to pieces in a salvage operation that took 10 weeks to complete.

Admiral Cecil Haney, commander of the US 7th Fleet, said its officers and watch teams used an "inaccurate" coastal chart for navigation even though more accurate ones were readily available.

"USS Guardian leadership and watch teams failed to adhere to prudent, safe, and sound navigation principles which would have alerted them to approaching dangers with sufficient time to take mitigating action," he said.

"Ultimately, the lack of leadership led to increased navigational risk to the ship and her crew," he concluded.

His report was posted on the US Navy website at 3:11 pm Thursday Honolulu time (0111 GMT Friday). The 7th Fleet is based in Hawaii.

The 68-metre (223-foot) vessel hit the reef while sailing for Indonesia after a visit to the Filipino port of Subic Bay.

The Philippines has demanded compensation for damage to the reef, a UNESCO World Heritage site in a remote area of the Sulu Sea.

The US government apologised and agreed to negotiate compensation.

The commanding officer, Lieutenant Commander Mark Rice and three other officers were relieved of their duties on April 3, with further administrative action still under consideration, the report said.

"This tragic mishap was wholly preventable and was the product of poor voyage planning, poor execution, and unfortunate circumstances," Haney said.

"The (officer of the deck) determined before grounding that the ship was closer to the South Islet of the Tubbataha Reef than expected based on the navigation plan, yet failed to take action to determine the ship's true position," the report added.

It also reconstructed in detail how the ship's hull eventually punctured, forcing its 79 officers and crew the following day to jump into rough seas that nearly drowned some of them.