The foreign ministry has told the consul to leave Turkey "for a period of time", the state-run Anadolu news agency said.
Turkey's foreign ministry has asked Israel's consul-general in Istanbul to leave the country "for some time", after Israeli forces killed more than 60 Palestinians during protests in the Gaza Strip.
At least 62 Palestinians were killed and thousands more injured by Israeli forces along the Gaza border Monday.
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Turkish President Recep Tayyip Erdogan, now on a visit to Britain, had on Monday stepped up his rhetoric, accusing Israel of "state terror" and "genocide" over the killings.
Ankara has been a vocal critic of the Israeli violence against Palestinians in Gaza and the opening of the United States embassy in Jerusalem.
On Monday, Erdogan, who is in London for three-day official talks, spoke to Palestinian leader Mahmoud Abbas over the phone.
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In a tweet titled "Reminder to Netanyahu", Erdoğan then denied that Hamas is a terror group, saying it is a "resistance movement that defends the Palestinian homeland against an occupying power".
Last week, the Israeli government said the ongoing border protests constituted a "state of war" in which global humanitarian law did not apply.
Turkey has responded to the violence by asking the Israeli ambassador to leave the country, while also recalling its ambassadors to the USA and Israel "for consultations".
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Earlier, Yıldırım invited his counterparts from five countries to join an emergency summit of the Organization of Islamic Cooperation (OIC) on the killings of Palestinians at the Gaza border.