"Three servicemen sustained lethal injuries as a result of the attack," Russia's Western Military District said in a statement carried by Interfax.
The statement noted the armed assailant had escaped, following the attack that began in the early hours of Monday.
"The command of the military unit, acting together with law enforcement agencies, is working to track down and detain the assailant," it said.
The National Guard of Russia spokesman confirmed to Sputnik that a search had been launched in Voronezh to find the attacker.
However, Russian media offered conflicting reports about the serviceman was holed up in a room at the Baltimor military airfield in Voronezh.
The reports suggested that negotiations were underway with the suspect who had locked himself in a building for his surrender to authorities.
According to preliminary reports, the perpetrator, identified as 20-year-old conscript Anton Makarov, seized a rifle from an officer while wielding an axe and subsequently opened fire on his fellow servicemen.
The shooting was sparked by an altercation between the soldier and the officer during an inspection, according to an unnamed Interfax source.
The soldier "grabbed a handgun" from the officer's holster and fired, the source said.
Last year, a Russian soldier, who had complained about compulsory military service describing it as "hell", opened fire on troops at a military base in Siberia, killing eight soldiers and injuring two others.