Col. Alexander Drobyshevsky said Jr. Sgt. Alexander Glukhov had been taken to Tbilisi.
The Georgian Interior Ministry said Glukhov had left his unit over the weekend, surrendered to Georgian police and requested political asylum.
Drobyshevsky dismissed the Georgian claim as a provocation and said Russia urged Georgia to release Glukhov immediately.
"Whatever statements Glukhov might have made must have been given either under physical or moral duress," he said.
The Georgian Interior Ministry has said the Russian serviceman is to undergo "a course of psychological and medical rehabilitation," whereupon the question of granting him political asylum "will be considered without fail."