The country's national security agency and the Prosecutor's Office suspect an 88-year-old man of crimes against humanity between 1945 to 1949.
Harrys Puusepp, a spokesman for the Internal Security Service, told uudised.err.ee on Tuesday that Pavel Boitsov's alleged crimes include participating in the systematic persecution, incarceration and murder of civilians by state authorities.
According to the agency, Boitsov was a translator and fighter in a task force which attacked and interrogated civilians, including members of the anti-Soviet resistance.
The task force, which was under the jurisdiction of the interior ministry of the Estonian Soviet Socialist Republic, operated between 1945 and 1946 in Võru County in southern Estonia.
Boitsov allegedly took part in at least two attacks on farms in which 15 civilians were killed, and in a number of other operations between 1946 and 1949.