Zacarias Moussaoui was arrested in the United States in August after flight instructors grew suspicious because he wanted to learn how to steer a plane - but not how to land or take off.
Questions are now being asked about why his arrest did not lead US investigators to uncover the 11 September hijack plot.
French security sources say they told the Federal Bureau of Investigation (FBI) of his suspected links with extremist groups - and that he had spent time in Afghanistan.
Immigration charges
FBI director Robert Mueller said the authorities had decided in August that they lacked legal authority to search Mr Moussaoui's computer.
He was then being held on immigration charges.
It was later found to contain information on flight training and crop spraying from planes.
His inquiries about hiring a crop duster plane are now being seen as possible evidence of a plot to spread chemical, biological or radioactive material in an American or western city.
French tip-offs 'ignored'
Security sources in Paris say British police turned down French requests to question him in the 1990s - when he espoused radical Islam as a student in London.
The sources said French authorities had alerted UK police after they detected that he had travelled to Afghanistan and Pakistan, the sources said.
The US indictment made public on Tuesday alleges that he spent time in terrorist training camps in Afghanistan.
Mr Moussaoui is alleged to have made the same preparations as the 19 hijackers suspected of carrying out the attacks.
Financial links alleged
He is also said to have received money from the al-Qaeda network led by Osama Bin Laden - the man accused of masterminding the attacks.
In a letter to his mother published by a French newspaper in November, Mr Moussaoui denied involvement in the attacks. He said he feared that a case was being fabricated against him.
Watching television in detention, he is reported to have cheered when he saw the hijacked planes smash into the World Trade Center and the Pentagon.