The ministry did not provide details on the location of the meeting in the Syrian capital.
Fidan had announced on December 20 that he planned to travel to Damascus to meet the new Syrian leaders who ousted strongman Bashar al-Assad after a lightning offensive.
Turkish spy chief Ibrahim Kallen earlier visited the city on December 12, just days after Assad's fall.
Kallen was filmed emerging from the Umayyad Mosque in Damascus surrounded by bodyguards.
Turkey has been a major supporter of the opposition to Assad since the uprising against his rule began in 2011.
In addition to supporting various rebel groups, it hosts Syrian dissidents and millions of refugees.
But Fidan rejected US President-elect Donald Trump's claims that the rebels' victory in Syria represented a "hostile takeover" of the country by Turkey. | BGNES