Andrei Lysenko also said Ukrainian troops had been fired upon by missiles from a village just inside Russia, the Associated Press reported.
Officials in Kiev have recently accused Russia's armed forces of being directly implicated in attacks on Ukrainian troops battling an insurgency near the border.
Lysenko said in a televised briefing that the pilot of the Sukhoi-25 jet that was hit on Wednesday evening was forced to bail out after his jet was shot down. He provided no further details.
Pro-Russia rebels, meanwhile, claimed responsibility for Wednesday strikes on two Ukrainian Sukhoi-25 jets.
The Defense Ministry said the second jet was hit by a portable surface-to-air missile, but added the pilot was unscathed and managed to land his plane safely.
Moscow denies Western charges that is supporting the separatists in Ukraine or sowing unrest in its neighbor.