The appointment, expected to be announced later this month, is an important step in Turkey's push to join the European Union.
Two senior diplomats have been named as candidates for the post of secretary-general of the NSC after the general who has held it for the past year was appointed Second Army commander on Thursday.
EU governments have in effect demanded that Turkey put a civilian in charge of the council to reduce military interference in political affairs. For years, the military-dominated council has steered Turkish policy on such crucial issues as Cyprus, Iraq and the Kurdish insurrection of the 1980s and 1990s.
Turkey's EU candidacy will be intensely discussed in Brussels over the next few months ahead of a December summit when the 25 member states must decide whether to start formal entry talks with Ankara.
Suat Kiniklioglu, director of the Ankara Centre for Turkish Policy Studies, said: This is a very symbolic move because it will show that critical positions in the decision-making process are filled by civilians, just like in an ordinary democracy.
The fact that the post will be filled by someone who does not wear a uniform is an important signal that things are changing in Turkey.
The two diplomats who are candidates for the post are Umit Pamir, Turkey's permanent representative to the United Nations and former ambassador to Greece, and Osman Koruturk, the country's special representative to Iraq and former ambassador to Germany.
Diplomats said Mr Pamir appeared to be the favourite, although both men are widely considered to have the backing of the military and the government. Turkey has experienced three military coups since 1960, while in the late 1990s the military engineered the collapse of an Islamic-oriented government without resorting to force.
The NSC is a constitutionally mandated body with a majority of its membership made up by generals. It became the symbol of the deep state that Turks believed wielded effective power while squabbling coalition governments came and went.
Under reforms being pushed through by the ruling Justice and Development party, the NSC's influence will be reduced, while that of parliament is expected to be enhanced.
Some senior officers are said to see this as an inevitable part of democratisation in Turkey, although diplomats say others may seek to reverse it if Ankara is snubbed by the EU in December.
General Sukru Sariisik, who stepped down as NSC secretary-general on Thursday to take up his new appointment with the Second Army, was among several top generals whose roles were redefined at a meeting of the military high command.
Yasar Buyukanit was named commander of land forces. This makes him the most likely successor to General Hilmi Ozkok, the chief of the general staff, who is regarded as a liberal and a supporter of Turkey's entry into the EU.
