This video frame shows Recep Tayyip Erdogan (right) receiving EU Council President Charles Michel (centre) and President of EU Commission Ursula von der Leyen (left) at the Presidential Complex in Ankara. Turkish Presidency/AFP

Gender equality issues took center stage on Wednesday in Brussels a day after Ursula von der Leyen, one the EU's most powerful executives, was treated like a second-rank official during a visit to Ankara.

The European Commission hit out after its chief Ursula von der Leyen was left without a chair as Turkey's president sat down for talks with her male counterpart.

Von der Leyen — the European Commission president — and European Council chief Charles Michel visited Turkey on Tuesday for talks with Turkish leader Recep Tayyip Erdogan focusing on the EU-Turkey relations.

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Video from Tuesday's encounter in Ankara showed von der Leyen flummoxed as Recep Tayyip Erdogan and European Council president Charles Michel took two chairs in front of the EU and Turkish flags.

"Ehm," she muttered, holding out her arms in apparent exasperation.

The European Commission president Von der Leyen prepares to speak with the media. File photo

After they were led to a big room for discussions with Erdogan, TV images showed that only two chairs had been laid out in front of the EU and the Turkish flags for the three leaders.

Eventually she was seated on a sofa a little further away from her counterparts, opposite Turkey's foreign minister -- someone below her in the pecking order of diplomatic protocol.

A Turkish official told AFP on Wednesday: "No arrangements were made other than those requested by a preliminary EU delegation which prepared the visit."

Von der Leyen, as president of the European Commission, is head of the EU executive. Michel, president of the European Council, represents member state governments. Brussels expects both to be treated with the protocol reserved for a head of government.

"The president of the commission was clearly surprised," European Commission spokesman Eric Mamer said, insisting von der Leyen should have been treated "exactly in the same manner" as Michel.

"She does consider that these issues are important and need to be treated appropriately, which they clearly were not," Mamer said.

The faux pas -- quickly dubbed "sofagate" online -- came at a delicate moment, as the EU and Turkey look to rebuild ties despite concerns over Ankara's record on human rights, including discrimination against women.

Erdogan angered Brussels ahead of the visit by the bloc's chiefs by announcing he was withdrawing Turkey from the Istanbul Convention on preventing violence against women and children.

Speaking after the meeting with the Turkish leader, von der Leyen stressed that "human rights issues are non-negotiable".

"I am deeply worried about the fact that Turkey withdrew from the Istanbul Convention" said the former German defence minister.

"This is about protecting women, and protecting children against violence, and this is clearly the wrong signal right now."

Spokesman Mamer said that the problem surrounding von der Leyen's seating during the meeting with Erdogan had "sharpened her focus on the issue".

The perceived slight to the first woman ever to occupy one of the EU's top two roles raised hackles back in Brussels.