The foreign ministry's statement came a day after Russia accused Turkey of breaching the Open Skies treaty by refusing the plane access.
"An agreement could not be reached on the itinerary for the reconnaissance flight requested by the Russian Federation for 2-5 February 2016," the ministry said.
Moscow said yesterday that the Russian plane's itinerary had been transmitted to the Turkish army in advance but authorisation was refused with Ankara.
Its aim is to boost mutual understanding and confidence.
In an apparent bid to downplay the significance of the latest incident, the Turkish foreign ministry said today it had allowed Russia to conduct a reconnaissance flight in December after Moscow changed the itinerary as requested by Ankara.
The latest salvo in an ongoing dispute between the two countries came some three months after Turkey shot down in November a Russian fighter jet on the Syrian border, sparking a war of words with Moscow which insisted its plane had not violated Turkish airspace.
Ankara on Saturday accused Moscow of a new violation of its airspace by a Russian Su-34 plane, a claim that Moscow dismissed as "baseless propaganda.
