Justice Minister Cemil Cicek formally requested that a court overturn the decision to release Agca, after weeks of raging debate on whether the 48-year-old former hitman had served less time than he should for crimes he committed in Turkey before his release on Thursday.
After nearly 25 years in jail, most of it in Italy, Agca was set free thanks to sentence reductions in the form of a series of amnesties and other reductions foreseen in the penal code, but experts say deductions from his jail term have been miscalculated.
In his letter to the appeals court, carried by the Anatolia news agency,
Mr Cicek argued against a court decision to deduct the time Agca served in Italy from his Turkish jail sentence.
He also added that the deduction was made on the grounds that Agca had served 20 years in Italy, for the attack on the pope, when in fact he had served only 19 years and one month.
Journalist murder
The minister said that Agca still had to serve a reduced 10-year sentence for the 1979 murder of a prominent journalist, arguing that the said sentenece could not have been deducted from his overall jail time.
The former extreme right-wing militant "has not earned the right to parole", Mr Cicek said.
Former justice minister Hikmet Sami Turk, who oversaw Agca's extradition from Italy in 2000, said he should have remained in jail until 2012 even with the most generous calculation of his sentence reductions.
Agca's lawyer Mustafa Demirbag, however, claims his client should in fact have been released earlier than January 12.
Touted in the press as the country's most notorious killer, Agca was released from a high-security prison in Istanbul on Thursday to a hero's welcome laid out by his supporters and a furious public outcry.
He had been incarcerated in Turkey following his extradition from Italy where he served 19 years for his assassination attempt on the pope on May 13, 1981.
He shot and seriously wounded John Paul II but the pontiff later visited him in prison and publicly forgave him.
Armed robberies
In Turkey, Agca was sentenced to seven years for two armed robberies in the 1970s and was also supposed to serve a reduced 10-year sentence for murdering prominent Turkish journalist Abdi Ipekci, the chief editor and columnist of the liberal daily Milliyet, in 1979.
But he was released after serving only five and a half years due to the series of sentence reductions.
On Wednesday, a Turkish military hospital declared Agca unfit for military service, which is obligatory for all Turkish men over 18.
The hospital did not say why Agca had been declared unfit.
Agca's attorney said the hospital had decided against recruiting Agca into the military on account of his lengthy jail time.