Turkish police picked up Agca in Kartal, a district on the Asian side of Istanbul, the city governor Muammer Guler said.
There was no reaction from the current head of the Roman Catholic Church. "We will not make any comment," Vatican spokesman, Joaquin Navarro Valls, told the Italian news agency ANSA.
Earlier the Turkish Court of Cassation ruled unanimously that Agca's release on January 12, after nearly 25 years behind bars in Italy and Turkey, should not have been allowed, the semi-official Anatolia news agency said.
The court went along with a request from Turkey's Justice Minister Cemil Cicek, after weeks of debate on whether the 48-year-old former hit man had served less time than he should for crimes he committed in Turkey before his release, including the murder of a well-known journalist, Avdi Ipekci.
Mehmet Agca was set free thanks to a series of amnesties and other sentence reductions allowed in the penal code, but experts said the deductions from his jail term had been miscalculated.
The 48-year-old was hardly seen in public after he was set free from jail.
When taken back in custody and brought to police headquarters in Istanbul, Agca, handcuffed and escorted by several police officers, shouted to a crowd of waiting journalists.
"I am the Messiah, I am the Messiah. I am not God, I proclaim the apocalypse," he said. The scene shown on several Turkish television channel also showed him speaking in English: "I am the Christ. I am not God."
Similar remarks were reported earlier this week in a Turkish newspaper which published excerpts of letters Agca reportedly wrote during his last few years in prison.
He claimed to be the reincaration of Jesus Christ and also offered to assassinate Al-Qaeda chief Osama bin Laden, prompting speculation over his mental state or whether he was just playing the madman.
Reaction to his re-arrest from the ruling Justice and Development party came from Sadullah Ergin, vice president of the parliamentary group, who said the court's decision "repaired" the lower court's action which "was troubling to public opinion" in Turkey.
His lawyer Mustafa Demirbag said on NTV that they would respect "all decisions by the independent Turkish court."
Former justice minister Hikmet Sami Turk said earlier he should have remained in jail until 2012 even with the most optimistic calculation of his sentence reductions.