State and Navy divers have determined that the $1 billion warship USS Port Royal damaged a coral reef when it ran aground half a mile south of the Honolulu Airport's reef runway earlier this month.

“;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 Department of Land and Natural Resources Director Laura Thielen in a joint news release with the Navy. “;Divers from our Division of Aquatic Resources 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.”;

The Navy also faces the possibility of hefty fines since coral is protected by state and federal laws. Deborah Ward, DLNR spokeswoman, said it is “;premature”; to talk about fines until the joint state-Navy investigation is completed and reviewed by state attorneys. Last year, DLNR fined a Maui tour boat company $550,000 for damaging coral in the waters of Molokini islet.

In addition, the Navy says now that 7,000 — not 5,000 — gallons of waste water were dumped while the ship was aground Feb. 5-9 to prevent it from backing up and endangering the crew.

State and Navy divers will spend another week moving debris from the grounding area to deeper water and reattaching large pieces of coral.

The Navy had originally failed to tell the state and public about the waste-water discharge, even though two Health Department officials attended a meeting with Navy officials at Pearl Harbor on Feb. 8.

The Navy said the waste water consisted mostly of sea water, used to flush waste.

“;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,”; said Rear Adm. Joseph Walsh, deputy commander of the Pacific Fleet. “;We regret this unintentional grounding, and we are glad that we were able to refloat the ship without injury to the crew while minimizing environmental harm.”;

The dumping took place on Feb. 6 after a Navy barge was unable to transfer the waste water and fuel from the 9,600-ton guided-missile cruiser because of rough seas. The Navy said the Port Royal's crew made every effort to mitigate the effects, including shutting off water to showers and sinks to minimize the released amounts.

The Port Royal was taken to Pearl Harbor Naval Shipyard's dry dock on Wednesday for repairs. When the grounding occurred, the vessel had begun sea trials after spending six months in the shipyard undergoing $18 million of repairs, maintenance work and repainting.

Although there has been no official damage report or estimate on the cost to repair the cruiser, Walsh has said that water leaked into the sonar dome located below the bow. Also, several of the 10 propeller blades were sheared off.

Photos released by the Navy show scrapes along the hull and at least five blades missing.

Initially, the Navy insisted the area where the ship ran aground in 20 feet of water consisted mainly of rocks and sand.

State and Navy divers from Pearl Harbor's Mobile Diving and Salvage Unit 1 have been in the water since Feb. 12, tagging and replacing broken coral blocks.

The divers concentrated this week on mapping and photographing the extent of the damage to identify coral colonies that might be reattached to the reef using quick-setting cement.

Thielen said the department developed undersea survey and mapping techniques from two groundings in 2005: the Cape Flattery at Barbers Point and the Casitas at Pearl and Hermes reef in the Northwestern Hawaiian Islands.

Navy and state divers also are noting the locations of detached reef blocks or other debris that might roll in the surf and cause additional damage to the reef over time.

These are being removed by Navy divers and disposed of at a deep-water site approved by the state.

The removed rocks range from 2 to 5 feet in diameter.

The Navy has not decided the fate of Capt. John Carroll, Port Royal's commander, or any of the sailors who were on watch on the ship's bridge at the time of the grounding.