Prime minister Kyriakos Mitsotakis described Turkey's decision as a sign of 'weakness'. Protests are expected in Athens and Thessaloniki.
Protests took place across Greece on Friday following Turkey's decision to reconvert Istanbul's Hagia Sophia into a Muslim place of worship.
Hundreds prayed and sang to the sound of the bouzouki in Athens' Kolokotroni square, holding banners reading "No to new Ottomanism" and denouncing "the second capture of Constantinople by the Turks".
Another rally with some 150 people was staged in Thessaloniki, Greece's second-largest city.
The ancient building and UNESCO World Heritage site of Hagia Sophia went through several changes throughout the centuries.
Inaugurated in 537 as a Christian cathedral, it became a Mosque in 1453 following the Ottomans' conquest of Constantinople (Istanbul) and the subsequent fall of the Eastern Roman/Byzantine empire.
It then was converted into a museum by Turkey in 1934, as part of its efforts to become a secular state.
But things were set to change once more as only a few weeks ago Turkish president Erdoğan announced the iconic building would be turned back into a mosque following a High Court ruling saying Hagia Sophia's museum status was illegal.
The decision was not welcomed well in neighbouring Greece.
On Friday afternoon, when the cathedral reopened to the faithful, church bells rang in mourning across Greece and flags flew at half-staff.
The head of the Church of Greece, Archbishop Ieronymos II, called the reconversion an "ungodly defiling act", adding that today is "a day of mourning for all of Christendom".
The Patriarch will hold a special mass in the Athens Cathedral in the evening, during which he is expected to sing the Christian-Orthodox Akathist hymn for the Virgin Mary; a chant believed to have been first sung in the year 626 to thank the Virgin for protecting Constantinople during an Ottoman siege.
Greek prime minister Kyriakos Mitsotakis told reporters on Friday that what's happening at Hagia Sophia is "not a manifestation of power" but a "sign of weakness"
After receiving the Patriarch of Alexandria Theodore II, the Prime Minister also called for turning "sadness into strength, composure and unity."
"Because Hagia Sophia exists precisely to unite us all, inviting us to look higher", he said, adding that "our hearts beat there."
Greek government spokesman Stelios Petsas said in an interview with private channel Open TV that Turkey's move "will create an unbridgeable gap between Turkey and the Christian world.”