Lotfi Raissi (right) arrives in court
Twenty-seven-year-old Lotfi Raissi faces extradition to the US after British police re-arrested him on an international warrant on Friday.
His detention is the latest development in the international effort against terrorism.
Six Algerians arrested in Spain on suspicion of links with Osama Bin Laden, considered by the US as the prime suspect in the attacks, are been held for further questioning by the high court in Madrid.
Spanish police say they found videos belonging to the suspects which contained images of attacks in Algeria and Chechnya and training camps in Afghanistan.
Lotfi Raissi was among four people arrested in the UK last Friday.
"He was a lead instructor of four of the pilots that were responsible for the hijackings," prosecutor Arvinda Sambir told Friday's court hearing in London.
She said Mr Raissi had trained the hijackers of the plane that crashed into the Pentagon.
'Conspiracy to murder'
Mr Raissi visited the US on a number of occasions between June and July this year "to ensure that pilots were capable and trained" for the hijackings, the court heard.
The warrant from the FBI details charges of obtaining a pilot's licence dishonestly but more charges are likely.
"It is no secret that conspiracy to murder is being looked at," Mr Sambir told the court.
But Mr Raissi's defence counsel, Richard Egan, said his client adamantly denied any involvement in the attacks and was "confident he would be absolved of all involvement".
Mr Raissi's wife and brother were also arrested by London police but subsequently released without charge. Another man is being held but has not been charged.
Meanwhile, police in Leicester in the English Midlands continue to question three men in connection with alleged plans to attack the US embassy in Paris.
Identities mystery
In the US, the Federal Bureau of Investigation has appealed for more information on the 19 suspected suicide hijackers who carried out the four attacks on 11 September.
Photographs of the suspects have now been published on the FBI's website, but the US investigators admit that some of the identities remain a mystery and they are still trying to confirm their real names.
More than 300 people have now been detained in the US, but so far no charges have been laid against anyone in connection with the hijackings.
'Hijacker's final instructions'
The US Justice Department believes at least eight of the 19 suspects may have been Saudi nationals.
FBI Director Robert Mueller said the authorities were trying to determine "whether, when these
individuals came to the United States, these were their real names or they changed their names for use with false identification in the United States".
Investigators have found a handwritten document left behind by one of the suspects - Mohamed Atta - which included Islamic prayers and instructions for a last night of life, the Washington Post reports.
The five-page document, written in Arabic, contained practical reminders to bring "knives, your will, IDs, your passport" and to "make sure nobody is following you". It was found in a piece of luggage that did not make it onto Atta's fatal flight, the paper said.
The document said that "only those, the believers who know the life after death and the reward after death, would be the ones who will be seeking death".