"The zones do not affect the routes that operate flights to Simferopol and to Crimea as a whole," Okulov said on the sidelines of the 10th international Transport of Russia forum.
The deputy minister said it was unfortunate that Moscow's "appeal to common sense" was left unheeded by Kiev.
"This is a sad situation, the fact that we have not been heard. It is definitely not conducive to coordinating our actions on air traffic over neutral waters in the Black Sea," Okulov stressed.
The Russian Defense Ministry summoned Ukraine's defense attache last week to serve a note protesting Ukraine illegally restricting the use of airspace over the Black Sea during the December 1-2 missile firing drills near Crimea.
Ukrainian Air Force's Air Command South said Thursday that the missile firings' nearest approach point to the Crimean peninsula does not exceed 18.6 miles.
