The incident came after Ukraine carried out an audacious coordinated drone attack on Russian airbases last week that damaged billions of dollars worth of nuclear capable military planes.
The National Guard said it detected a man "preparing a terrorist attack using a drone" at a military facility in the Ryazan region, southeast of Moscow.
"During the arrest, the criminal gave armed resistance and was neutralised," the agency said in a statement.
It published surveillance footage of a hooded man crouched in a field trying to launch a drone before being chased by armed officers. It does not show him being shot.
In the attack last Sunday, Ukraine smuggled small remote-operated quadcopter-style drones deep into Russian territory in false roofs of wooden cabins.
Loaded on to trucks, they were driven up close to Russian airbases and then released simultaneously to attack the sites.
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