The Palestinian-Jordanian cleric was first arrested for alleged terror connections in 2001.
Qatada, 53, was tried and convicted in abstentia in 1999 in Jordan on two charges of conspiracy to cause explosions, court documents said.
He is facing a retrial in Jordan for an alleged bomb attack plot that targeted American and Israeli tourists during Jordan's millennium celebrations, the BBC reported.
Britain fought to deport him for eight years and was only able to do so after it signed a treaty with Jordan that stipulated evidence against him obtained through torture would not be used to convict him.
"This dangerous man has now been removed from our shores to face the courts in his own country," British Home Secretary Theresa May said Sunday.
"I am also clear that we need to make sense of our human rights laws and remove the many layers of appeals available to foreign nationals we want to deport," May said. "We are taking steps -- including through the new Immigration Bill -- to put this right."
May said she did not have any concern about how Qatada would be treated after he arrived in Jordan.
"The treaty we've signed ensures that there are proper processes of exchange of evidence and will insure the treatment of Abu Qatada and others deported to Jordan," May said.
British Prime Minister David Cameron said he was "delighted" Qatada was off British soil.
The BBC quoted Cameron saying it "made my blood boil that this man who has no right to be in our country, who is a threat to our country and that it took so long
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