The meeting chaired by Turkish President Recep Tayyip Erdogan at the presidential complex in capital Ankara lasted for five-and-a-half hours.
A statement issued after the meeting read: "The activities carried out to maintain public order and peace and security of our citizens, the stage [the country] reached regarding fighting terrorism and terrorists, and the measures taken against the Parallel State Structure which threatens our national security were discussed."
Headed by Fetullah Gulen, a U.S.-based preacher who runs a network of schools and commercial enterprises in Turkey and around the world, what is known as the “parallel state” allegedly represents a clandestine group of Turkish bureaucrats and senior officials, embedded in the country’s institutions, including the judiciary and the police.
The meeting was the first for Binali Yildirim as new prime minister and his cabinet, which was announced on Tuesday.
The statement said the terror organization PKK and its political affiliate could not represent Kurdish citizens living in Turkey, referring to the People's Democratic Party (HDP), which is represented in parliament.
The PKK - designated a terrorist organization by Turkey, the U.S. and the EU - renewed its armed campaign against the Turkish state this summer.
Fighting the Daesh terror organization was also discussed in the meeting.
"The fighting against Daesh and its attacks against our country were discussed, and the necessity of implementing a no-fly zone and safe zone cleared of terror was put forward once more."
Ankara has long called for a safe zone in northern Syria to protect civilians from airstrikes.