No one was hurt when gunmen opened fire on the unarmed aircraft, a spokesman said. The Diamond light aircraft was flying three crew on an observation mission, the spokesman said.
Russian forces took control of Crimea last week. Pro-Moscow separatists have declared the region part of Russia and plan a referendum for March 16 to confirm it.
Moscow says it has no troops in Crimea beyond those normally stationed there with its Black Sea Fleet, an assertion ridiculed by the West.