Lebanese security officials refused to say when and where Bakri was arrested.
Prosecutors and police in Britain are considering whether to bring terror-related charges against the so-called "Tottenham Ayatollah".
It was unclear whether the arrest was linked with his activities in the UK.
Bakri provoked outrage last week when he said he would not inform police if he knew Muslims were planning a bomb attack.
He left Britain, where he has lived for 20 years, on Saturday and travelled to the Lebanon to see his mother, his spokesman has said.
The preacher - spiritual leader of the soon-to-be-banned al-Muhajiroun group - said he planned to return to London in about four weeks.
But on Tuesday it emerged that immigration rules could be tightened within weeks to bar him from setting foot in the country again.
Deputy Prime Minister John Prescott admitted the Government was currently impotent to stop him returning, although he made his own feelings clear.
"As I understand it, he has not committed an offence under the existing legislation. I just say enjoy your holiday, make it a long one," Mr Prescott said.
The Attorney General's office said at the weekend that the Crown Prosecution Service and the Metropolitan Police were considering reviving the ancient offence of treason to prosecute Bakri and two other Muslim clerics.
However, this has since been denied by Director of Public Prosecutions, Ken Macdonald QC, and dismissed as unlikely by the Lord Chancellor, Lord Falconer of Thoroton QC.
Bakri is Syrian, but his wife's family is Lebanese and he has citizenship in both Syria and Lebanon.Reuse content