An American ship captain was freed unharmed on Sunday in a swift firefight that killed three of the four Somali pirates who had been holding him for days in a lifeboat off the coast of Africa, the ship’s owner said.

A senior US intelligence official said a pirate who had been involved in negotiations to free Captain Richard Phillips but who was not on the lifeboat was in custody. Phillips, 53, of Underhill, Vermont, was safely transported to a Navy warship nearby.

Maersk Line Limited President and CEO John Reinhart said in a news release that the US government informed the company around 1.30 pm EDT on Sunday that Phillips had been rescued. Reinhart said the company called Phillips’ wife, Andrea, to tell her the news. The US official was not authorised to discuss the matter publicly and spoke on condition of anonymity.

When Phillips’ crew heard the news aboard their ship in the port of Mombasa, they placed an American flag over the rail of the top of the Maersk Alabama and whistled and pumped their fists in the air.

Crew fired a bright red flare into the sky from the ship. A government official and others in Somali with knowledge of the situation had reported hours earlier that negotiations for Phillips’ release had broken down.