Speaking in Tokyo, Mr Obama said Mohammed, the self-proclaimed organiser of the al-Qaeda terrorist plot that killed almost 3,000 people in 2001, would face “exacting” US justice.

Bringing such notorious suspects to US soil to face trial would be a key step in Mr Obama’s plan to close the US detention centre at Guantanamo Bay.

Mr Obama initially planned to close the centre at the US naval base on Cuba by Jan 22 next year, but his administration is no longer expected to meet that deadline.

It is also a major legal and political test of Mr Obama’s overall approach to terrorism. If the case suffers legal setbacks, the administration will face second-guessing from those who never wanted it in a civilian courtroom.

The New York case may force the court system to confront a host of difficult legal issues surrounding counter-terrorism programmes begun after the 2001 attacks, including the harsh interrogation techniques once used on some of the suspects while in CIA custody. The most severe method – waterboarding, or simulated drowning – was used on Mohammed 183 times in 2003, before the practice was banned.

The US attorney general Eric Holder is due to annonce that a major suspect in the bombing of the USS Cole, Abd al-Rahim al-Nashiri, will face justice before a military commission, as will a handful of other detainees to be identified at the same announcement, an official said.

The transfer of the detainees from Guantanamo to New York is not expected to happen for many more weeks because formal charges have not been filed against most of them.