By 1964, Ismet Inonu who had represented Turkey at the Lausanne Conference in 1923 and had been Kemal Ataturk's close ally was Prime Minister. Following ethnic fighting in Cyprus, the Prime Minister took action against the remaining Greeks of Turkey, who had nothing to do with the Greek-Turkish conflict whatsover. Prime Minister Inonu renounced the Greek-Turkish Treaty of Friendship and then took action against the Greek minority,

"Over a thousand Greeks were promptly expelled, most on a few hours' notice. They were permitted to take with them only $22 and one suitcase of clothes. Another 5,000 were expelled shortly thereafter. Another 10,000 to 11,000 Greeks were expelled after September 1964, when Turkey discontinued renewing residence permits of Greek citizens. On October 11, 1964, The Turkish newspaper Cumhurriyet, reported that 30,000 Turkish nationals of Greek descent had left permanently,in addition to the Greeks who had been expelled." "Denying Human Rights & Ethnic Identity. The Greeks of Turkey. Helsinki Watch. A division of Human Rights Watch. March 1992.

With the bulk of Turkey's Greeks having been expelled from Turkish soil, the wrath of Ankara now aimed at the Patriarchate. During the mid and late 1960's the Turkish government threatened to expel the Patriarchate from Turkey. Pressure from the United States kept Turkey from taking such a step. According to Turkish writer Tozun Bachelli in his "Greek-Turkish relations since 1955": "There were fears that if the Patriarchate, as the center of Orthodox Christianity was removed from Istanbul, the Soviets might use the Russian Orthodox Church to assume a position of leadership and larger influence among the Orthodox Christians. This may very well have served as an added restraint to Turkey in it's deliberations over the possible expulsion of the Patriarchate."

"But in the 1960's the Turkish government placed restrictions on the Patriarchate and threatened to remove it from Turkey. Two senior Churchmen were expelled and the Patriarchate's printing house was ordered closed". Denying Human Rights & Ethnic Identity: The Greeks of Turkey. Helsinki watch, A division of Human Rights Watch. March 1992.

"An extremely serious problem for the Patriarchate is the closing of the Halki Patriarchal school of theology, the academy that, between 1844 and 1971, trained clergy for the Ecumenical Patriarchate". Denying Human Rights & Ethnic Identity: The Greeks of Turkey".Helsinki Watch, A division of Human Rights Watch. March 1992.

"The authorities monitor the activities of Eastern Orthodox Churches and their affiliated operations. The Ecumenical Patriarchate in Istanbul has consistently expressed interest in reopening the Seminary on the island of Halki in the Sea of Marmara. The Seminary has been closed since the 1970's when the state nationalized most private institutions of higher learning".TURKEY. Country Reports on Human Rights practices for 1996. Department of State. February 1997.

"The Turkish Government vetoed today the candidacy of Archbishop Iakovos of New York as a possible successor to Patriarch Athenagoras I. A Foreign Ministry spokesman said the Archbishop was not acceptable because of his United States citizenship". New York Times. July 9, 1972.

"A 1976 New York Times article "Beleaguered Greeks in Istanbul Fearful of Future" numbered the Greeks in the city at 15,000.Helsinki Watch estimated them at 2,500 when it travelled to Turkey in the fall of 1991."The following are examples of the climate of oppression Greeks face and are taken from the publication "Denying Human Rights & Ethnic Identity: The Greeks of Turkey". Helsinki Watch, a division of Human Rights watch. March 1992.

"Greeks in Istanbul told Helsinki Watch of being harassed by police-called in and threatened."

"According to ethnic Greeks, the Turkish government does not permit newspapers or magazines published in Greece to be imported into the country, and no Greek books are available in bookstores."

"Helsinki Watch concludes that the Greek minority has been denied equal treatment in education and the right to control it's schools, in violation of international human rights agreements, the Lausanne Treaty and the Turkish Constitution".

"Helsinki Watch concludes that the Turkish government has denied the Greek community in Turkey the right to express it's ethnic identity, in violation of international human rightslaws and agreements".

"The ministry of education tightly controls the curriculum in foreign language schools. Many Greek origin students report difficulty in continuing their education in Turkey and go to Greece, often never to return". TURKEY. Country Reports on Human Rights practices for 1996. Department of State. February 1997.