The accident happened Monday evening near the Krasnodar region, RIA Novosti reported.
The ministry initially reported the pilot had survived after ejecting safely.
"At 8:32 a.m. [local time] the ground search and rescue team found the body of the pilot in the area where the Su-25 came down," Defense Ministry spokesman Igor Konashenkov said.
"According to reports from the accident site the pilot tried to land the aircraft on open ground after he had guided it away from nearby towns. The aircraft exploded on contact with the ground," he added.
Military investigators said they've opened an inquiry into whether any flight rules were broken or if there were violations in the preparation of the aircraft that could have led to the accident.
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