"My thoughts go to Istanbul. I think of Santa Sophia and I am very pained," he said during his weekly blessing in St. Peter's Square, Reuters reported.
Turkish President Tayyip Erdogan has said the first prayers would be held in Hagia Sophia on July 24, after declaring the ancient monument was once again a mosque following a court ruling revoking its status as a museum.
The World Council of Churches has called on Erdogan to reverse his decision and Patriarch Bartholomew, the Istanbul-based spiritual leader of the world's Orthodox Christians, called it disappointing.
Erdogan said the nearly 1,500-year-old Hagia Sophia, which was once a Christian cathedral and then a mosque for hundreds of years, would remain open to Muslims, Christians and foreigners.
He added that Turkey had exercised its sovereign right in converting it to a mosque and would interpret criticism of the move as an attack on its independence.
Greece has condemned the move and UNESCO said its World Heritage Committee would review Hagia Sophia's status and that Turkey's decision raised questions about the impact on its universal value as a site of importance transcending borders and generations.