A Turkish man who hijacked a flight from Albania and demanded that it be flown to Rome was facing arrest in Turkey for avoiding army service.
Passengers were allowed off the plane after hours of questioning
Hakan Ekinci was being flown from Albania to Turkey after his asylum application was turned down.
The plane was forced by Italian fighter jets to land at Brindisi in southern Italy on Tuesday, where the unarmed hijacker surrendered.
Mr Ekinci, a Christian convert said he wanted to give a message to the Pope.
The plane's passengers were flown on to Istanbul on Wednesday.
Most of the 107 passengers were Albanians, who had caught the Turkish Airways plane flying from Tirana, Albania to Istanbul on Tuesday.
Also on the passenger list were contestants in an international beauty pageant in Albania, including Miss India, Miss Singapore, Miss Malaysia and Miss Philippines.
"The reason he insisted on landing in Rome or in Brindisi was to get a missive to the Pope," Italian Interior Minister Giuliano Amato said on Wednesday.
Turkish convert to Christianity
Absconded from Turkish army, fled to Albania
Wrote to Pope, seeking help in his bid for asylum
Asylum refused by Albania, which sent him back to Turkey
The hijacker slipped into the cockpit after the door was opened by flight attendants, Mr Amato said.
The man handed the pilot a note, saying he wanted to deliver a message to the Pope, and referring to accomplices with a bomb.
Mr Amato said it turned out, however, that the man had no accomplices.
A search revealed he had no written message for the Pope either.
"The peculiar thing about this hijack was that it was done by a lone, unarmed man," he said.
The minister said the incident was worrying, ahead of the Pope's visit to Turkey at the end of November, a trip which he said would "present delicate security problems".
The hijacker was named as Hakan Ekinci, 28, who had fled from the Turkish army and run away to Albania.
He reportedly said he was a convert to Christianity who could no longer be forced to serve in a Muslim army.
He had apparently sought political asylum in Albania, and had written a letter to the Pope in the past pleading for his help in gaining asylum.
He charted his efforts to gain asylum in letters to a well-known Turkish pacifist group on the internet.
The Turkish foreign ministry confirmed to the BBC that the hijacker was on the run from the army.
Separately, Istanbul Governor Muammer Guler said that Mr Ekinci had faced arrest and transfer to the military authorities on arrival in Istanbul.
It was initially reported that the plane had been hijacked by Turks protesting at Pope Benedict XVI's forthcoming trip to Turkey.
The trip has come under tight scrutiny, especially following comments the Pope made last month interpreted as linking the spread of the Islamic faith with violence.
However the Vatican said the hijacking was not expected to affect the Pope's plans.