One of the EU's most senior officials on Friday condemned Turkey's reconversion of the Hagia Sofia into a mosque, warning that Ankara was undermining its ties with Europe.

"As a Greek, I'm quite bitter. I'm feeling quite angry about it," said Margaritis Schinas, a European Commission vice-president, at a press briefing.

His comments came as Turkish President Recep Tayyip Erdogan led the first Friday prayers at Istanbul's Hagia Sofia since it was reconverted from a museum into a mosque. 

"I think that Turkey at a certain point should decide what their geopolitical stance should be, and who they want to align themselves with in the future," warned Schinas, going further than the EU's statements of concern to date.

"Will Turkey want to work along with the European Union and base themselves on European values? And, if that's the case, what's happening today with the Hagia Sophia is really a bad starting point."

The UNESCO World Heritage site was first built as a cathedral in the Christian Byzantine Empire and its historic association with the Greek Orthodox church means the reconversion has further strained Turkey's relations with NATO ally Greece.

The Hagia Sophia was converted into a mosque after the Ottoman conquest of Constantinople in 1453, and a Turkish court ruled this month that it remained a mosque in its property deeds, opening the way for a return to Muslim worship.