The court, acting on an appeal by the Justice minister, ruled Agca should not have been released early from a Turkish prison where he was serving a 10-year sentence for bank robbery and murder.
Agca, 48, spent 20 years in prison in Italy for shooting the pope in St. Peter's Square 25 years ago.
The BBC said Agca was picked up in Istanbul Friday and taken to police headquarters.
Agca's release last week caused anger in Turkey and the government said he should serve his full sentence for the 1979 killing of a journalist and two bank robberies.
Pope John Paul publicly forgave Agca for shooting him when he visited him in prison in 1983.