Midhat Guler, who was placed under house arrest last week, was put on a plane to Turkey on Thursday.
"This expulsion is due to the threat the person concerned poses to public order," an Interior Ministry statement said.
"Mr Guler is in effect in charge in France of an extremist Islamic Turkish movement that advocates resorting to violence and terrorism known as 'Kaplan'," it said.
France, whose five-million-strong Muslim community is Europe's largest, has about 1500 Islamic prayer leaders. Most are poorly trained and many speak only Arabic.
The French government has stepped up efforts to promote imam training centres so that prayer leaders preach an Islam compatible with a modern Western democracy.
Last month, the government experienced an embarrassing setback when a court ruled as illegal its decision to expel an imam from the southeastern city of Lyon after he justified wife-beating in a magazine article.
Abd al-Kadir Buzian, who holds French nationality, was expelled to his native country of Algeria on 21 April and had his French resident's permit confiscated.
But on Monday, he said he had been given a visa allowing him to return to France.