The state for the first time yesterday confirmed there was significant damage to coral reef caused by the 3 1/2-day grounding of the guided missile cruiser USS Port Royal this month off Honolulu Airport's reef runway.

The Navy, meanwhile, released photos of the 9,600-ton warship in drydock showing damage to its propellers, sonar dome and scrape marks on a hull that just months ago had been repainted a bright blue.

The ship ran aground Feb. 5 half a mile off the reef runway, and was freed Feb. 9.

Divers noted detached coral reef colonies, which are being tagged for possible reattachment using quick-setting cement, the state and Navy said in a joint release yesterday.

Some blocks of reef up to 5 feet in diameter that could roll in the surf and cause more damage are being removed by Navy divers and disposed of in deep water.

The largest blocks are being cemented in place to stabilize them and prevent further movement, according to the release.

"Although initial reports indicated that the ship had grounded on a rock and sand bottom, our subsequent surveys have shown that there is, in fact, coral reef," said Laura H. Thielen, chairwoman of the state Department of Land and Natural Resources.

State divers "are now working in cooperation with counterparts from the Navy to ensure that no further damage occurs, and to map the full extent of the grounding scar," Thielen said in the release.

The state divers have been in the water since Feb. 12, conducting an underwater survey of the grounding site. DLNR spokeswoman Deborah Ward yesterday said she couldn't provide an estimate of the size of the coral reef area damaged.

Robert Harris, director of the Sierra Club Hawai'i Chapter, said the concern is that some coral species take decades, if not centuries, to grow back fully.

"We have a fair amount of reef around the island, but the corals have been under increasing stress due to increasing temperature of the water and other manmade effects," Harris said. "So there's been increasing concern about what's going to happen to reefs."

The DLNR can seek fines for coral damage; in January 2008 the department fined a Maui tour boat company $550,000 for damaging coral in the waters of Molokini Islet. It was unclear yesterday whether fines would be pursued against the Navy.

CREW KEPT SAFE

Rear Adm. Joseph A. Walsh, deputy commander of U.S. Pacific Fleet, said in the release that the Navy regrets the grounding, but is glad the ship was able to be refloated without injury to the crew.

"Keep in mind that while the ship was aground for those 78 hours, the Navy was concerned foremost about the safety of the crew, freeing the ship and minimizing damage to the environment," Walsh said.

There was no oil leakage. Walsh said at a press conference following the grounding that the marine environment "has been described to me as a sand rock bottom ... but it has the potential to sustain life is how it was described to me."

The 567-foot Port Royal ran aground about 8:30 p.m. on Feb. 5 on its first day of sea trials after being in a Pearl Harbor Naval Shipyard drydock for about three months for $18 million in maintenance.

The Navy was unsuccessful in three attempts to pull the $1 billion warship off the reef in 17 to 22 feet of water, and its very public predicament just half a mile off the reef runway garnered the Navy a lot of unwanted public attention.

After removing 600 tons of weight — including 500 tons of seawater ballast and 40 tons' worth of anchors and anchor chains — the Navy lightened the ship enough to pull it backward from its perch around 2:40 a.m. on Feb. 9.

The incident heavily damaged the bow-mounted sonar housing and struts, shafts and propellers. Propeller blades were sheared off. The salvage ship Salvor, the Motor Vessel Dove and seven Navy and commercial tugboats were used to pull the Port Royal free.

The ship's commander, Capt. John Carroll, was temporarily relieved of his duties, pending the investigation outcome. The extent of repairs that are needed and bill for the work are still being determined, the Navy said.

As many as 42 sailors a day from the Navy's Mobile Diving and Salvage Unit One have been assisting the state effort, moving and reattaching large pieces of coral.

The Navy yesterday said 7,000 gallons of wastewater were released by Port Royal while it was aground to prevent the sewage from backing up into the ship. The state Health Department previously complained the Navy did not officially notify it of the release, which the state agency initially believed was 5,000 gallons.

Capt. W. Scott Gureck, a spokesman for U.S. Pacific Fleet, said there was a miscommunication during a time of hectic activity.

"This (the grounding) was an emergency situation where people could have died," he said. "The focus was on keeping people alive and keeping a ship from breaking up and causing incredible environmental harm."