Abdiwali Abdiqadir Muse has been jailed in Manhattan since he was captured last year and faced what was called the first US piracy prosecution in decades.
"What we did was wrong," a subdued Muse said through an interpreter Tuesday. "I am very, very sorry about what we did. All of this was about the problems in Somalia."
He also pleaded guilty to hostage-taking and conspiracy.
He faces a minimum 27 years in prison. Sentencing was set for Oct. 19.
Prosecutors branded Muse the ringleader of a band of four pirates who provoked a deadly drama by targeting the Maersk Alabama on April 8, 2009, as it transported humanitarian supplies about 450 kilometers off the coast of Somalia.
The case could be the first of several piracy prosecutions in US courts. It's part of a larger US policy debate over how best to deal with the insurgents and criminal activities that contribute to the persistent instability in Somalia, a poor and chaotic country that's become a haven for Al-Qaeda-linked terrorists.
In the Maersk Alabama case, a criminal complaint said Muse was the first to board the ship, firing his AK-47 assault rifle at the captain, Richard Phillips. He entered the bridge, told the captain to stop the ship and "conducted himself as the leader of the pirates," the complaint said.
Muse, reading from a prepared statement, told the judge on Tuesday that his crew had not intentionally targeted an American vessel. The four pirates "agreed to capture any ship that we found on the Indian Ocean," he said.
The pirates held Phillips hostage for several days on a sweltering, enclosed lifeboat that was soon shadowed by three US warships and a helicopter.
During hostage negotiations, Muse said, the pirates tried to cut a deal: "They get the captain back and they let us go back to land safely. If not we will harm the captain." The end came when Navy sharpshooter on the USS Bainbridge picked off the three pirates in a stunning nighttime operation, leaving Phillips untouched.
"I thought the pirates were shooting one another, and I was caught in the crossfire," Phillips later wrote in a book about his ordeal. "They'd been arguing, and it had escalated to gunfire. And now, after days of heat, punishment and threats, there was complete silence.
"All of a sudden I heard a voice. A male American voice.
‘Are you OK?' it said."
After being swept into a federal court into New York, the skinny, 5-foot-2 defendant looked bewildered and sometimes wept in court. His age was in dispute from the start: His lawyers insisted he was 15 and should be tried as a juvenile; prosecutors convinced a judge he was at least 18.
Back in Somalia, Muse's parents insisted he was tricked into getting involved in piracy. His mother said he was "wise beyond his years" and never a troublemaker.
Somalia is an impoverished nation caught up in a violent Islamic insurgency and has had no effective government or justice system since 1991. Piracy has become a multimillion-dollar business, and attacks have continued despite the presence of about 35 international warships patrolling nearby waters.
Many countries refuse to prosecute pirates, and suspects picked up at sea often are released after their weapons are seized.
The US Navy has taken into custody more than 20 suspected pirates in the violence-plagued waters off Somalia and nearby regions, where US warships are part of an international anti-piracy flotilla.
US officials have said they hope to bring federal charges against some of the other suspects. There also have been preliminary discussions about setting up a special international court, because a number of countries will not act against suspected pirates who are turned over to them.
