People pose for photographs in front of the Byzantine-era Hagia Sophia in Istanbul, on Friday. AP

Turkey on Saturday lambasted Greek statements against the move to convert Hagia Sophia back into a mosque after the first Muslim prayers were held in the Istanbul landmark.

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Relations between NATO allies Ankara and Athens have been uneasy in recent months but tensions increased over Hagia Sophia and energy riches in the eastern Mediterranean.

Turkish President Recep Tayyip Erdogan joined thousands for the first Islamic prayer on Friday since Hagia Sophia was reconverted from a museum into a mosque this month.

Protesters burn a Turkish national flag outside of a church during a gathering in Thessaloniki against turning the historic Hagia Sophia in Istanbul. AFP

Greek prime minister Kyriakos Mitsotakis on Friday said what was happening in Istanbul was "not a show of force, but proof of weakness".

The reaction to Hagia Sophia opening for Muslim worship "once again revealed Greece's hostility towards Islam and Turkey," Turkish foreign ministry spokesman Hami Aksoy said.

Aksoy "strongly condemned" the burning of the Turkish flag in Thessaloniki, and accused the Greek government and parliament of "provoking the public with hostile statements".

"The spoiled children of Europe, who cannot accept renewed prostration in Hagia Sophia, are once again delusional," Aksoy added in a statement.

Huge faithful attend the Friday prayers at Hagia Sophia Grand Mosque in Istanbul. AFP

The UNESCO World Heritage site was originally the Byzantine Empire's main cathedral before its conversion into a mosque after the Ottoman conquest of Constantinople in 1453.

The founder of modern Turkey ordered Hagia Sophia to be turned into a museum in 1934 but Turkey's highest administrative court on July 10 said the building was registered in property deeds as a mosque, allowing Ankara to change its status once more.

Turkey and Greece's ties are also strained over the issue of migration, especially after Ankara re-opened its border for refugees to leave for Europe earlier this year.