Less than six hours after Agca walked out of the high-security Kartal prison, Justice Minister Cemil Cicek said he would order a review of the case, as a debate raged among jurists over whether his release was legally sound.
Mr Cicek hinted that the 48-year-old Agca, who served 19 years in Italy for shooting and seriously wounding the pope and was convicted for separate crimes in Turkey, including the 1979 murder of prominent journalist Abdi Ipekci, might be put back in jail.
"The fact that he (Agca) was released today does not constitute a reserved right for that person," Mr Cicek told reporters, describing the case as "extremely complicated."
"In order to eradicate the doubts, I will use my right to a written order" to the Court of Appeals to review the case.
Former justice minister Hikmet Sami Turk, who oversaw Agca's extradition to Turkey in 2000, and Ipekci family lawyer Turgut Kazan both condemned his release as a grave judicial error.
He should be released in 2012 at the earliest, even if he is entitled to the most favorable reductions and amendments, Mr Turk told CNN-Turk television.
Freedom
Wearing a blue sweater and jeans, a gaunt and graying Agca emerged from the main building of Kartal jail surrounded by a dozen armed soldiers.
With a solemn look on his face, the former member of the notorious far-right Grey Wolves climbed into a white car as nationalist sympathizers showered the vehicle with red and yellow flowers.
Activists from the Turkish Communist Party, sworn foes of Agca's Grey Wolves in the 1970s, were also outside the prison, demonstrating against his release and holding portraits of slain fellow leftists.
Agca was taken straight to an army recruitment office because the authorities still accuse him of evading military service, which is compulsory for all Turkish men over 18.
His lawyer has said he will ask for an arrangement under which Agca will pay a hefty sum in lieu of military service, or ask to be exempted on health grounds.
From the recruitment office, Agca was taken to the Istanbul suburb of Tuzla, home to a major infantry training camp, and then to the GATA military hospital, after which he disappeared from sight.
Agca told the authorities he would live in Pendik, a suburb on Istanbul's Asian side, where he will report twice a day to police, officials told the Anatolia news agency.
"He is very calm and happy," Agca's lawyer, Mustafa Demirbag, told Anatolia.
"We are doing what the law requires," Mr Demirbag said. "Mehmet Ali Agca is now a free man."
He played down suggestions that Agca's life may be in danger.
Pope gunman
Agca served 19 years in Italian prisons for the May 13, 1981, attack on John Paul II in St Peter's Square.
He was a 23-year-old militant Grey Wolf, on the run from Turkish police, when he opened fire on the pope who was driving to an audience in an open vehicle.
John Paul II, who was seriously wounded in the abdomen, forgave Agca when he met him later in prison.
Agca has claimed his attack was part of a divine plan and has given contradictory statements, frequently changing his story and forcing investigators to open dozens of inquiries.
His motives remain to this day shrouded in mystery.
The late John Paul II wrote in his last book, "Memory and Identity", that he was convinced the assassination attempt was highly planned and that Agca was a mere puppet.
Pardoned by Italy and extradited to Turkey in June 2000, Agca was also serving time for two bank robberies committed in the 1970s and for the 1979 murder of Abdi Ipekci, a prominent editor and columnist with the daily Milliyet.
Agca would have served 36 years, but was freed under reductions that accompanied amnesty laws and European Union-inspired reforms to the Turkish penal code that cut prison terms for the crimes of which he was found guilty.