The Higher Military Council (YAS) ended a three-day meeting with a decision that it would keep control of the secretariat of the National Security Council (MGK) in spite of a vote by the Turkish parliament last week to limit the political influence of the armed forces.
It will make a formal statement on Monday. But, according to CNN-Turk, Deputy Prime Minister Mehmet Ali Sahin has accepted that it is "possible" that a senior military figure could head the permanent secretariat "for a transitional period".
On Wednesday the parliament passed a package of reforms to curb the powerful army's influence in politics, a key demand of the European Union for the opening of membership talks with Turkey.
The package limits the powers and areas of responsibility of the MGK, the country's top policy-making body through which the generals exercise their influence in politics, and the council's secretariat, which is dominated by the army.
The council is made up of the president, prime minister, defence, interior, foreign and communications ministers and the five most senior officers in the armed forces to "lay down priority recommendations to the government". It meets once a month.
The package agreed by the parliament provides for the possibility that a civilian could head the secretariat and lays down that the MGK should meet no more than once every two months.
Press reports said that Prime Minister Recep Tayyip Erdogan had agreed to a request from the chief of the general staff Hilmi Ozkok before the YAS met to leave a military figure at the head of the secretariat.
Limiting the military's powers is a task of particular difficulty for the governing Justice and Development Party (AKP), a conservative movement whose Islamist roots have caused suspicions among the military, the self-declared guardians of secularism in the Muslim nation.
According to Mehmet Ali Sahin, the decision to leave the military at the head of the MGK was in conformity with the new law as it has not yet been promulgated by the president.
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