Germany has deported a Moroccan man who acted as a "book-keeper" for the 9/11 terrorists, 17 years after the deadly attacks.

Mounir el Motassadeq, a member of a terrorist organisation known as the called "Hamburg cell", was imprisoned in 2006 after he was convicted of aiding lead hijacker Mohamed Atta and two other al-Qaeda extremists by paying their tuition and rent to keep the pretence that they were students.

Almost 3,000 people were killed when two hijacked planes were flown into the twin towers of New York's World Trade Centre on 11 September 2001. Two more jets were taken over by terrorists, one crashing into the Pentagon and the other into a field in Pennsylvania.

El Motassadeq, who had protested his innocence during the 2006 trial, is now expected to be put on a flight to Marrakesh, Morocco, after being collected from his Hamburg jail cell, where he had served almost 15 years.

The 44-year-old was flown by helicopter to the airport on Monday, and then escorted by two heavily armed police officers into a waiting area pending the afternoon flight, news agency dpa International reported.

Frank Reschreiter, the Hamburg Interior Ministry spokesman, said el Motassadeq would "leave the country soon" but would not specify exactly when he would be returned to Morocco over fears it could jeopardise the transfer.

Moroccan Mounir El Motassadeq at a court in Hamburg (AP)

"All the necessary procedural steps for this have been ticked off according to plan," Mr Reschreiter said.

El Motassadeq, who was raised in a middle-class family, came to Germany in 1993 to study engineering. It was here that he met Atta.

He became a suspect after German police realised he held power of attorney over a bank account belonging to Marwan al-Shehhi, the terrorist who flew United Airlines Flight 175, a Boeing 767-200, into the south tower of the World Trade Center.