The accident occurred on Monday while the son, 6, and his friend, 4, were left playing at the older boys home by his mother. The older boy took his father's gun and shot the other boy in the chest at point-blank range, unaware that the gun was loaded.
The four-year-old was killed instantly.
His father, 35, who bought the gun from a friend and did not register it with the local police department, faces charges of negligently keeping a firearm and ammunition.
Prosecutors will also carry out checks to see whether the boy was looked after properly by his parents.
Police have launched a probe into local social security authorities, who are charged with determining whether children are at risk.
According to Russian law, children under the age of 14 cannot be tried for murder.
