The US surveillance plane had its transponders turned off during Sunday's incident near the Russian border, the defence ministry said, adding that the crew had not informed regional authorities of the plane's route.
The plane used the same flight levels as those typically used by passenger jets, Moscow said, adding that "the unprofessional actions" of the US crew had created a risk of collision with other aircraft.
The defence ministry said measures needed to be taken to prevent such incidents in the future.
Ties between Russia and the West have plunged to their lowest point since the Cold War over Moscow's 2014 annexation of the Crimean peninsula from Kiev and its support for separatist rebels in eastern Ukraine.
