On Tuesday, Israel expelled the Turkish consul in Jerusalem after Ankara called back its ambassador to Israel and expelled the Israeli ambassador to Turkey.
Turkey has been among the most vocal critics of the Israeli use of deadly force against protesters at the Gaza border and of the U.S. decision to open its new embassy in a ceremony attended by President Donald Trump's daughter Ivanka and son-in-law Jared Kushner.
The tragic scenes overshadowed Mrs May's meeting at 10 Downing Street with Turkish President Recep Tayyip Erdogan.
The ministry said in a written statement that it expressed discomfort to Deniz over alleged mistreatment during the departure from Turkey of Eitan Naehe, Israel's ambassador to Ankara.
Israel expelled the Turkish consul-general in Jerusalem, and Erdogan exchanged heated words on Twitter with Prime Minister Benjamin Netanyahu.
Turkey also summoned Israel's Consul-General in Istanbul and demanded that he leave the country until further notice.
The 2016 reconciliation deal ended a dispute over the May 2010 deadly storming of a Turkish ship by Israeli commandos that saw relations downgraded.
"The synergy which will occur when Turkey's operational opportunities and the UK's financial power come together will bring very big benefits to both sides", Erdogan said.
Erdogan, who regards himself as a champion of the Palestinian cause, 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.
After talks with British Prime Minister Theresa May, Erdogan warned that history "will not forgive" Israel or the U.S. for moving the American embassy to Jerusalem in defiance of outrage in the Islamic world. Erdogan regards himself as a champion of the Palestinian cause and a year ago hosted an OIC summit in Istanbul to denounce US President Donald Trumps decision to recognise occupied-al-Quds as Israel's capital.
"America says "I am strong and so I am right". Which leaders may attend Fridays meeting has yet to be made clear. Erdogan, who is campaigning for presidential and parliamentary elections next month, said a rally will be held on Friday to protest the killings. At least 2,400 more were wounded in the bloodiest day in the Israeli-Palestinian conflict since the 2014 Gaza war.