US Navy snipers killed three Somali pirates who had been holding an American merchant skipper on a lifeboat last night, rescuing the hostage unharmed.

The US Navy Seals opened fire from about 25 metres away under standing orders from President Obama when they saw one of the pirates pointing an AK47 at Captain Richard Phillips’s back, putting his life in imminent danger.

All three pirates were killed. A fourth, who had come aboard a nearby US warship to negotiate, was taken into custody. He was reported to be as young as 16.

Captain Phillips, a former Boston taxi driver who was taken hostage on Wednesday after the crew of his cargo ship repulsed a pirate attack, was “resting comfortably” on a US Navy vessel last night after talking to his wife in Vermont.

The rescue took place at 5:19pm London time as the guided missile destroyer USS Bainbridge towed the drifting lifeboat to safer waters in deteriorating weather conditions.

US Vice-Admiral William Gortney said: “The sniper’s position on the fantail of the Bainbridge observed one of the pirates in the pilot house with [another] two pirates with their head and shoulders exposed. One of the pirates had their AK47 levelled at the captain’s back.

“The on-scene commander thought that the captain was in imminent danger and then made that decision, and he had the authority to make that decision and he had seconds to make that decision,” Vice-Admiral Gortney said in a videoconference from the US Fifth Fleet headquarters in Bahrain.

Captain Phillips, who was tied up in the 18ft covered lifeboat, was picked up by a US Navy launch and transferred from the USS Bainbridge to the USS Boxer, where he underwent a routine medical examination.

Vice-Admiral Gortney said that Captain Phillips declined an offer of food, and added that he believed he was in good health. The US Navy released a photograph of the bearded skipper with a broad smile and a clean set of clothes shaking hands with the commander of the USS Bainbridge following his release.

The dramatic denouement of the hostage crisis will come as a huge relief to President Obama, who had refused to comment on the stand-off as domestic criticism increased.

“I am very pleased that Captain Phillips has been rescued and is safely on board the USS Boxer,” Mr Obama said. “His safety has been our principal concern and I know this is a welcome relief to his family and his crew.

“I am also very proud of the efforts of the US military and many other departments and agencies who worked tirelessly to secure Captain Phillips’s safe recovery.”

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