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The kidnapped captain of the Maersk Alabama has been rescued and is safe aboard a U.S. Navy ship, U.S. officials said.

The U.S. Fifth Fleet, based in Bahrain, said the rescue of Capt. Richard Phillips took place shortly after 7 p.m. local time Sunday, according to a release sent by the command.

Getty Images

Capt. Richard Phillips, right, stands alongside Cmdr. Frank Castellano after being rescued Sunday.

The Navy said Capt. Phillips had been flown to the USS Boxer, an amphibious assault ship, where he called his family, went through a medical examination and was now resting.

U.S. sharpshooters killed three pirates holding Capt. Phillips after concluding that he was in "imminent danger," a U.S. commander said.

Vice Adm. William E. Gortney, commander of all naval forces in the Middle East, told a Pentagon news conference that the USS Bainbridge had been towing the lifeboat holding the pirates and Capt. Phillips into calmer waters when Navy Seal sharpshooters, positioned at the tail of the ship, saw the head and shoulders of the three remaining pirates, with one of them pointing an AK-47 machine gun at the head of Capt. Phillips.

Adm. Gortney said the Navy officer in charge of the operation ordered the pirates to be fired upon.

Before the incident, Adm. Gortney said U.S. officials had hoped to resolve the standoff peacefully. A fourth pirate was on the Bainbridge as part of hostage negotiation talks. But Adm. Gortney said tensions escalated between the pirates and negotiators, prompting commanders to believe Capt. Phillips, who was tied up on the lifeboat, was at risk of getting killed.

Adm. Gortney said he had received standing orders from President Barack Obama to rescue Capt. Phillips if the hostage's life appeared in danger, and the officers on the ship acted on that authority. No specific order from higher command came signing off on the shooting.

Sailors on the USS Bainbridge had been in regular contact with the four pirates and Capt. Phillips, shuttling food, water and clean clothes to the lifeboat aboard a small inflatable boat throughout the standoff.

Adm. Gortney said he could not confirm early reports that Capt. Phillips had prompted the final showdown by jumping from the life boat. He said the lifeboat was only about 25 meters behind the Bainbridge during the towing, giving the sharpshooters a better view of the boat.

"It got heated and the on-scene commander interpreted hostile intent," Adm. Gortney said.

Capt. Phillips: 'Heroes Are the Navy, the Seals'

John Reinhart, president and chief executive of Maerk Lines Ltd., called the captain's release a "truly, truly wonderful moment." Mr. Reinhart said he spoke with Capt. Richard Phillips, whom he described as "feeling quite good. He's getting some rest and he'll soon be home." He said Capt. Phillips wanted to relay the following message to the public: "John, I'm just the byline. The heroes are the Navy, the Seals and those have brought me home."

Mr. Reinhart called Capt. Phillips "a leader of men, a brave and courageous man" who "exhibited the true spirit of an American."

President Obama, responding to rescue of the Maersk Alabama's captain, said the U.S. must work with allies to interdict pirates and bring to justice those who are captured.

In a statement, Mr. Obama said the safety of Capt. Phillips had been the principal concern of the U.S. Mr. Obama praised the U.S. military and others involved in the rescue Sunday.

The president saluted the captain, saying: "His courage is a model for all Americans." He added: "We remain resolved to halt the rise of piracy in this region." A White House official said Mr. Obama spoke with Capt. Phillips at 4 p.m. Washington time.

Under federal law, the U.S. can bring any captured pirates back to the United States for prosecution, said Frank Wiswall, past chairman of the legal committee of the International Maritime Organization. Federal law states that "whoever, on the high seas, commits the crime of piracy as defined by the law of nations, and is afterwards brought into or found in the United States, shall be imprisoned for life."

"If it were my call, I would say bring them back here and try them here," Mr. Wiswall said.

Pirates attacked the Maersk Alabama, a U.S.-flagged merchant ship Wednesday. The crew regained control hours later, but pirates fled with Capt. Phillips as a hostage.

The Maersk Alabama pulled into Mombasa late Saturday. As the news of his release leaked out Sunday, the ship's horn blared three times. Shortly afterward the crew, which had avoided reporters all day, unfurled a big American flag and shot off a red flare that popped and lingered overhead the East African port.

Maersk officials said they were notified of the captain's rescue by U.S. officials at 1:30 pm Eastern time today. Mr. Reinhart called Capt. Phillips' wife to deliver the news.

Commenting on the crew of the Maersk Alabama, Mr. Reinhart said, "You should know that the crew was really challenged with the order to leave Richard behind. They didn't want to do it. They've expressed that throughout. But as mariners, they took the orders to preserve the ship and they knew the Navy would preserve their captain."

Several hours before the rescue operation, about seven crew members, clad in blue overalls and hard hats, watched from the railings as the ship pulled into its berth in Mombasa.

A few waved and one pumped his fist as the ship approached the dock. Several applauded the captain they were forced to leave behind.

"He's a hero," one of the ship's officers, Ken Quinn, shouted to reporters from the railing as the vessel pulled in. "The whole crew misses him. ... We owe the captain our lives."

The port was crawling with journalists wielding cameras and notebooks. A helicopter rented by the Associated Press hovered overhead. Security was tight. Several men in flak jackets, camouflage and automatic weapons moved about the ship.

The details of the pirate storming and the crew's actions are still sketchy. Agents from the Federal Bureau of Investigation and the Naval Criminal Investigative Service were still debriefing crew members Sunday and gathering evidence on the ship.

Associated Press

Security personnel guarded the Maersk Alabama, at port in Mombasa, Kenya, Sunday.

But short interviews with a handful of crewmembers over the weekend provide a rough outline of the attack.

The pirates came shortly before 7 a.m. on Wednesday. The ship's chief engineer, A.T.M. Reza, was the first to see them. A short, quick man with a black mustache, he said he was on deck, near the stern and watched the pirates speed toward the boat in a single skiff.

They tossed hooks over the side and began shimmying up the ropes, firing in the air as they went.

The attackers moved fast, and surprised much of the crew -- including waking Mr. Quinn up in his bed. Alerted to the boarding, other crew scrambled into a designated safe room aboard the vessel. Williams Rios, a crewmember from Manhattan, was one of them.

On deck, Mr. Reza said he volunteered to take one of the pirates, a small, scrawny man who identified himself as Abdul Mohamed, down to the engine room. When he got down there, the engineer overpowered him, thrusting an ice pick between the man's thumb and index finger in the struggle.

Other crew members quickly came to help. The pirate appeared shocked at the pain and frightened. The crew bound his hands and feet with rope, and locked him away in a secure room on the ship. The captured pirate turned out to be the band's leader, said Andrew Brzezinski, another crewmember.

The crew now had a bargaining chip. And while they didn't have guns, the Maersk Alabama's 20-man crew greatly outnumbered the four attackers. The crew demanded the other pirates leave the ship.

But the pirates had scuttled their own small boat. They demanded an escape boat, fuel and food. Amid the standoff, Capt. Phillips offered himself as a hostage to safeguard the crew.

"They agreed, and we agreed," said Mr. Brzezinski. "They promised to let go of the captain when we sent back the hostage."

Once the pirates settled into the lifeboat, the crew released their hostage. But the pirates refused to let Capt. Phillips free. "They wanted us to follow them to Somalia," said Mr. Brzezinski.

The crew continued to try to negotiate with the pirates but nothing worked, crewmembers said.

Several crewmembers said they were upset about turning back to Mombasa without their captain. "I can't describe my feelings," said Mr. Brzezinski.

Associated Press

The ship Maersk Alabama docks at port in Mombasa, Kenya on Saturday.

Bernard Odemba, a harbor captain in the Mombasa port, boarded the Maersk Alamaba Saturday evening when it arrived to help pilot the vessel in. Mr. Odemba said the crew told him the pirates had tried to damage the ship, smashing a few of the winches on the stern, or back, of the vessel. He said the crew was relieved to see him.

"They were still suspicious," he said, and nervous about other boats approaching the ship. "Whenever they saw any kind of boat...I had to calm them down."

Port security and American officials tried Saturday to seal off the ship to the throng of reporters that had gathered. They stacked rows of containers to partially block the ship.

Emotions were high after the ship arrived at the port. One crew member cursed at reporters.

"We've got a man out there in a lifeboat dying so we can live," he shouted. He hurled a coffee mug at a metal cargo container near the reporters, shattering it into pieces.

On Sunday, American officials boarded the ship again around 9 a.m. to meet with the men. The crew is expected to remain on the ship until officials finish gathering evidence for their investigation, officials said. That could take at least a few days.

Sunday morning, Mr. Rios wandered on deck for a smoke and explained to reporters what was going on inside the ship: "A lot of meetings," he said.

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