RIA Novosti said recent media reports alleged soldiers and officers in a unit on the Far East islands were given food that contained worms and then were forced to go hungry.
Eastern Military District spokesman Col. Alexander Gordeyev denied the claims Tuesday.
But Wednesday, the main military prosecutor's office confirmed an investigation was under way, including assessment of drinking water and sanitary requirements, RIA Novosti said.
Russia keeps forces on the islands, which Japan also claims, RIA Novosti said.
Scandals concerning the army's living conditions and poor food have been frequent in the last 20 years, RIA Novosti reported.