Muhammad Metin Kaplan, 51, was detained at an internet cafe in Cologne and put on board a Turkey-bound plane at the Duesseldorf airport on Tuesday even though he formally had two weeks to appeal the decision by the Cologne administrative court.
Kaplan faces charges for masterminding a failed 1998 plot to crash a plane laden with explosives into the mausoleum of Mustafa Kemal Ataturk, the founder of the modern secular Turkish state.
Angelika Flader, a spokeswoman for the North Rhine-Westphalia state interior ministry in Duesseldorf said the plane carrying Kaplan had taken off.
Germany has outlawed Kaplan's Caliphate State group, which calls for the overthrow of Turkey's secular government and its replacement with an Islamic state.
Kaplan had foiled police attempts to arrest him in May by disappearing for several days after another court ruled he could be extradited.
He was freed in May 2003 after serving a four-year German prison sentence for inciting others to kill a rival cleric in Berlin in 1997.
The Cologne court ruled that Kaplan remains "an identification figure for Islamic extremism" and that his interest in staying in the country is "outweighed by the public interest in an immediate deportation".
The court said that a pending appeal in federal court in Leipzig did not justify keeping him in the country and rejected his arguments that he was too sick to travel.