Activists in Manila scuffle with police Saturday after a U.S. Navy ship became grounded on a reef off the Philippines.

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A U.S. Navy minesweeper got stuck Thursday in a sensitive reef off the Philippines

It remained there Sunday, with no sailors aboard and its damage still not surveyed

A U.S. navy official says, " I greatly regret any damage this ... caused the Tubbataha Reef"

The reef, a World Heritage Site, contains threatened and endangered marine species

A U.S. Navy minesweeper remained stuck in a reef teeming with endangered marine life off the Philippines on Sunday, prompting an American commander to apologize and promise stepped-up efforts to prevent further damage.

The USS Guardian ran aground early Thursday in the Tubbataha Reef, about 80 miles east-southeast of Palawan Island in the Sulu Sea, the U.S. Navy reported.

All 79 sailors were evacuated from the 224-foot ship. Hazardous weather and rough seas have hindered efforts to survey the empty Guardian and the surrounding area, though the Navy acknowledges damage to the reef.

“As a protector of the sea and a sailor myself, I greatly regret any damage this incident has caused the Tubbataha Reef,” said Vice Adm. Scott Swift, the U.S. 7th Fleet commander, in a report posted Sunday on a Navy website.

“We know the significance of the Tubbataha Reefs Natural Park and its importance as a World Heritage Site. Its protection is vital, and we take seriously our obligations to protect and preserve the maritime environment.”

The Guardian, an Avenger-class mine countermeasures ship based in Japan, was heading from Subic Bay to its next port call in Indonesia when it struck the reef’s south atoll, the Navy said.

The incident remains under investigation.

Initial efforts to free the ship failed and its crew was transferred by small boats to other U.S. ships.

The U.S. Navy reported no signs of oil slicks in the area.

Philippine Navy spokesman Lt. Cmdr. Gregory Favic – in a report on the official Philippines News Agency (PNA) – similarly indicated no evidence of oil.

Three Philippine naval ships were in the area, along with a number of U.S. ships, according to Sunday’s PNA report.

The U.S. Navy will step up efforts on Monday when Rear Adm. Thomas Carney takes over as on-site commander on the destroyer USS Mustin.

The focus is “preventing any further environmental damage to the reef and surrounding marine environment,” according to the Navy report.

Home to a vast array of sea, air and land creatures, as well as sizable lagoons and two coral islands, Tubbataha Reefs Natural Park is a UNESCO World Heritage site.

About 500 species of fish and 350 species of coral can be found there, as can whales, dolphins, sharks, turtles and one of the last surviving colonies of breeding seabirds in the region, according to UNESCO.

CNN’s Brad Lendon contributed to this report.