Mounir al-Motassadek is accused of belonging to a terrorist organisation and assisting in the murder of more than 3,000 people.
German Federal Prosecutor Kay Nehm said Mr Motassadek, who is accused of being part of a Hamburg cell of Osama bin Laden's al-Qaeda network, is believed to have helped three of the hijack pilots enter the United States.
Mr Nehm said prosecutors had also prepared charges against three other alleged members of the Hamburg group.
The 28-year-old Moroccan, who was arrested in November 2001, is the first person to be charged in Europe in connection with the attacks.
Planned attacks
Mr Nehm said Mr Motassadek was part of a group which arrived in Hamburg from Arab countries between 1992 and 1997.
He lived in an apartment in the city near to that of alleged hijacker Marwan al-Shehhi and the suspected ringleader of the group, Mohamed Atta.
Mr Nehm said the alleged cell was planning an attack on the World Trade Centre in New York well over a year before last September's strikes.
Al-Shehhi, who is believed to have flown one of the hijacked planes which hit the twin towers, was said to have mentioned the World Trade Centre to a Hamburg librarian in April or May 2000.
Mr Nehm said al-Shehhi had added: "There will be thousands of dead, you will think of me."
Managed bank account
Mr Nehm said Mr Motassadek and other members of the cell flew to Afghanistan to organise the logistical details of the attacks and that the Moroccan received training from al-Qaeda in the city of Kandahar.
The suspects returned to Germany in early 2000, and the hijackers flew to the United States, where they began training at flight schools in Florida.
The federal prosecutor said Mr Motassadek helped three of the pilots enter the US and managed a bank account in the United Arab Emirates, which was used to finance the hijackers' flying lessons and living costs.
He said Mr Motassadek talked to Mohamed Atta on the telephone two days before 11 September and also signed his will.
Extremist ideology
Mr Nehm said the Hamburg group became radicalised in 1998 and adopted a philosophy rejecting western consumer culture.
He said the group was motivated by a hatred of the international Jewish community and a belief that it was their duty to convert non-believers to Islam.
In investigating the Hamburg cell, authorities had looked into the activities of other Islamic groups and examined a terrorist network including Italy, Spain, France and Great Britain.
German police are still hunting three other men who they say lived with Atta.
The three had reportedly tried to enter the United States but had been denied visas.