Turkey presented a note to Israel after recent remarks made by the Israeli Commander of Ground Forces Avi Mizrahi.
According to a statement issued by the Turkish Ministry of Foreign Affairs (MFA) on Saturday, Israeli Ambassador in Ankara Gabby Levy had been summoned to the MFA by the Undersecretary due to Mizrahi's comments, Anadolu Agency said.
Remarks against all forms of diplomatic practice, historical and current realities and those accusations as well as nonsensical talks targeting our prime minister and country had been protested by a note, the MFA said.
"Furthermore, we have stressed that the relevant statements of Avi Mizrahi are ungrounded and unacceptable and as such we have requested an urgent explanation from Israeli authorities," the MFA also said.
Turkish General Staff also issued a statement on Saturday in regard to recent comments made by Avi Mizrahi.
"The remarks made by the Israeli commander are unacceptable and could hurt national interests of Turkey and Israel," the Turkish General Staff said.
The Israeli Ground Forces Commander Mizrahi had made remarks accusing Turkey of the incidents of 1915.
The Turkish military also said that allegations by an Israeli general about Turkey's presence in Cyprus and its conflict with the Kurds threatened to harm relations between the two countries.
It was the latest sign of tension between Turkey and Israel, who maintain close military ties but whose alliance has been strained by the Israeli offensive on Gaza.
Turkish Prime Minister Tayyip Erdogan criticized Israeli President Shimon Peres of "knowing very well how to kill" in a public debate last month at the World Economic Forum in Davos, Switzerland.
Mizrahi was quoted by Haaretz newspaper as saying Turkey was not in a position to criticise Israel's occupation of Palestinian lands when it stations troops in northern Cyprus as a retaliatory to Davos.
Decades long armed attacks on the defenseless Turkish Cypriots culminated in 1974 when an Athens-backed Greek Cypriot military coup on the island led to Turkey's military intervention.
He also accused Turkey of repressing its Kurdish minority and massacring Armenians during World War One.
Turkey says many Armenians in fact served at the highest echelons of the Ottoman government and the Ottoman parliament.
Turkey said that the equally well documented massacres and ethnic cleansing of Ottoman Muslims in Eastern Anatolia committed directly or assisted by Armenian rebels, which were acknowledged by independent observers, are routinely ignored or denied today.
The Turkish General Staff, in a statement carried by the state-run Anatolian news agency, said Mizrahi's remarks were competely unacceptable.
Turkey and Israel's military co-operation includes allowing Israeli jets to use Turkish airspace for training.
Erdogan told Reuters on Friday there were no plans to halt that agreement.
Turkey keeps about 30,000 troops in Turkish Republic of Northern Cyprus.
Although the Republic of Cyprus as described in the 1959 agreements is no longer there, Greek Cypriots continue to enjoy this title and international recognition while the Turkish Republic of Northern Cyprus, a fully democratic government representing Turkish Cypriots, still suffers under an unfair political and economic blockade.
Scholars in Ottoman history generally agree that the Armenian deaths resulted from a multiplicity of causes, the letter said and listed these causes as inter-communal warfare, the conditions of the forced relocations, murder, famine, disease, deficient medical care and austere conditions of life during wartime.