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 had said Wednesday that the Russian plane's itinerary had been transmitted to the Turkish army in advance but authorization was refused with Ankara.
The 2002 Open Skies treaty, signed by over 30 nations including Russia, Turkey, the EU and the US, establishes a program of unarmed aerial surveillance flights giving all participants the ability to gather information about military forces and activities of concern to them.
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 Thursday it had allowed Russia to conduct a reconnaissance flight in December after Moscow changed the itinerary as requested by Ankara, AFP reported.
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.
Russia launched a massive air campaign in September against terrorists fighting to overthrow Syrian President Bashar al-Assad.
Ankara Saturday accused Moscow of a new violation of its airspace by a Russian Su-34 plane, a claim that Moscow dismissed as "baseless propaganda."