The pirates used small boats to attack the vessel for several hours
US crew members have retaken their hijacked ship but their captain is still being held by Somali pirates on a lifeboat, reports say.
Pentagon sources and relatives of the Maersk Alabama's 20 crew were earlier quoted as saying the ship was back under control after a struggle.
But later reports emerged that the captain was still in the hands of the hijackers, adrift in the lifeboat.
It was the sixth ship seized off Somalia in recent days.
It is reportedly the first time in 200 years that a US-flagged vessel has been seized by pirates.
The Associated Press reported that they had spoken to a sailor on board the Maersk Alabama who said the crew had retaken the vessel and one pirate had been captured.
But the unnamed sailor told AP that three of the pirates were now holding the captain hostage in a lifeboat.
The ship's owners later confirmed that the pirates were off the ship but holding the captain.
"We are working closely with the US military and other government agencies to continue to respond to this situation as it develops further and will provide additional information as we are able," Maersk said in a statement.
The ship was attacked by several small boats in the early hours of Wednesday in an incident apparently lasting for about five hours.
Maritime officials said the vessel took all possible evasive action before it reported that the pirates had boarded.
More than 130 pirate attacks were reported in 2008, including almost 50 successful hijacks.
Pirates typically hold the ships and crews until large ransoms are paid by the shipping companies - last year the firms handed over about $80m (£54m).
The huge increase in frequency of attacks has forced several navies to deploy warships in the Gulf of Aden to protect one of the world's busiest shipping lanes.