On May 15, Israel's ambassador to Ankara Eitan Na'eh was summoned to the Turkish Foreign Ministry, where he was asked to leave the country.
Earlier on Tuesday, Alistair Burt, the Foreign Office minister responsible for Middle East affairs, reiterated Britains commitment to a two-state solution to the conflict, and said it did not agree with the USA decision to move its embassy.
However Turkey also maintains full trade and diplomatic links with the Jewish state after a 2016 reconciliation deal ended a dispute over the deadly storming of a Turkish ship by Israeli commandos.
Thousands of Palestinians had gathered on Gaza Strip's eastern border to take part in protests marking the 70th anniversary of the founding of Israel - the Nakba ("Catastrophe") - and protest the relocation of the U.S. Embassy from Tel Aviv to Jerusalem.
Ankara reacted with fury to the clashes, which came on the same day the United States formally moved its embassy in Israel from Tel Aviv to Jerusalem in defiance of global criticism.
Erdogan, now on a visit to Britain, had on Monday stepped up his rhetoric, accusing Israel of "state terror" and "genocide" over the killings.
Turkish Prime Minister Binali Yildirim also said that Muslim countries should review their ties with Israel after Monday's violence. Erdogan this week has accused Israel of "genocide" and told Netanyahu he is leading an "apartheid state" while having the "blood of Palestinians" on his hands.
Israel's Prime Minister Benjamin Netanyahu said on Twitter Erdogan was in no position to "preach morality to us" because he supported the Palestinian Islamist movement Hamas which rules Gaza.
"May said that while it was right that those who sought to overthrow a democratically elected government were brought to justice, "it is also important that in the defence of democracy..."
Erdogan arrived in the United Kingdom on Sunday for a three-day visit.
Erdogan will on Friday host an emergency summit meeting of the Organisation of Islamic Cooperation (OIC) in Istanbul which he has said will send a "strong message to the world" on the whole issue.