The crew said they had regained control of the Maersk Alabama after it had been commandeered by Somali pirates. But one of the crew members later told reporters by satellite phone that the captain was still being held hostage in a lifeboat.
Pentagon officials could not confirm details and said the picture remained "murky". As night fell in East Africa a US warship from the anti-piracy task force was reported to be steaming towards the container ship's last known location.
The day began with news of the first act of piracy against US citizens in 200 years.
At that stage President Obama, on a flight out of Baghdad, appeared to be facing the biggest foreign policy challenge of his administration.
Within hours the picture was turned on its head after the US Department of Defence was contacted by Captain Joseph Murphy, the father of the hijacked ships second-in-command Shane Murphy.
An instructor at the Massachusetts Maritime Academy, he told officials that he had received a call from his son who told him the crew had "regained control" of the vessel.
Capt. Murphy senior teaches anti-piracy courses at the Academy and his son is a graduate of the same institution.
Days before the attack Shane Murphy had written on his Facebook profile: "These waters are infested with pirates that highjack [sic] ships daily. I feel like it's only a matter of time before my number gets called."
A crew member who was reached last night by the Associated Press said the crew had retaken control of the ship, but that some pirates were in a lifeboat.
The man who answered the ship's satellite phone was said to have an "American accent".
The ship's captain was said to be in the lifeboat with the pirates while his shipmates attempted to negotiate his release by offering his captors food.
It was unclear how many pirates were involved in the initial attack and if there were any non-American crew members aboard the ship.
The 17,000 ton, US-flagged and owned ship was taken approximately 280 miles southeast of the Somali port of Eyl, one of the major centres of pirate activity.
Several important questions remained unanswered last night. Chief amongst them was the staffing of the Maersk Alabama, apparently a container ship transporting food aid, but doing so with an all-American crew. In the modern maritime world of deregulated shipping the vast majority of the world's two million merchant seamen are from the developing world. It would be extremely unusual for the vessel to be crewed by 20 US citizens.
Piracy expert John Burnett said that he suspected that the US "crew" may have been military operatives taking part in a honey trap operation.
Washington has refused to comment on speculation surrounding the Maersk's cargo, mission and crew.
The US vessel belongs to Maersk Line Ltd based in Virginia and is part of the US maritime security programme and regularly carries freight for the US Department of Defence. There are concerns over the cargo being carried by the vessel as the Maersk Alabama is one of "nearly 50 ships in commercial and (US) government service, including vessels requiring Top Secret security clearances," according to the firm's own website.
Resurgent pirates off the coast of Somalia have hijacked six vessels in the last six days, ending hopes that the increased naval presence in the region had alleviated the crisis.
Despite the heavy international naval presence off the northern coast of Somalia, US forces admitted yesterday that their closest vessel had been more than 300 miles away at the time of the hijacking.
Lt. Nathan Christensen, a spokesman for the US Fifth fleet said the attack came south of the area where the navy has been patrolling.
"The area we're patrolling is more than a million miles in size. Our ships cannot be everywhere at every time," he said.
Andrew Mwangura, a maritime expert in Mombasa, Kenya said the Somali pirates were running "sophisticated operations", with intelligence on ships movements and the capacity to attack far out to sea using larger "mother ships" which can release high speed attack boats. The Somalis themselves are trained fighters with satellite communications and GPS devices.
Normally captured ships are anchored close to the shore of Somalia while the captors negotiate a ransom, a process that can take months.
Most governments have decided against direct military intervention in maritime hostage crises. However, French forces engaged pirates in two separate incidents last year. In the first they used helicopter to chase pirates overland, following the payment of a ransom for the luxury yacht Le Ponant, capturing several suspects now on trial in Paris. In a second incident, French commandoes stormed the captured yacht of a retired French couple, freeing them and killing one pirate.
A week of unusually heavy attacks appears to show the pirates have switched their attention to shipping in the Indian Ocean. Last year there were a record 134 attacks and 49 hijackings. So far this year, despite the military investment, there have already been 53 attacks and 15 sea-jackings.
The World Food Programme in Nairobi said that the cargo included emergency food aid being shipped to Kenya and Uganda.
The origins of the current piracy crisis lie in the collapse of the Somali state in 1991 and the subsequent free-for-all in its coastal waters where foreign vessels have plundered incredibly rich fishing grounds. Initial clashes between foreign trawlers and local fishermen escalated to the point that ransoms began to be paid in the late 1990s.
Illegal fishing has since swollen to epidemic proportions in an industry estimated to be worth hundreds of millions of pounds annually.
Since then as many as 1,200 pirates in an estimated six gangs have emerged. It has become one of the failed state's biggest earners with pirates raking in as much as USD150m last year, according to Mr Mwangura who has been close to many of the ransom negotiations.
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