"The flights of MiG-29 fighters have been suspended until further orders," the spokesman said.
A MiG-29 fighter crashed at 10:45 Moscow time (06:45 GMT) on Friday 60 kilometers (37 miles) from the Domna airfield in the Chita Region during a regular training flight.
The pilot ejected safely and was later hospitalized. He is in a satisfactory condition.
The Air Force said there were no reports of casualties or damage on the ground and a special investigation team had been sent to the crash site.
Friday's crash is the first reported occurrence in Russia involving a MiG-29 fighter in 2008, although two MiG-29s crashed in Kazakhstan and Azerbaijan earlier this year in separate incidents.
Last year, two Russian Air Force MiG-29 fighters were involved in a mid-air collision over the Rostov Region. Both pilots bailed out safely.