Meri, a former Communist official, was accused of organizing deportations of 251 Estonian civilians to Siberia in 1949. Estonian prosecutors said that the deportees were mainly women and children and that over 40 of them later died.
Meri admitted involvement, but denied organizing the deportations, saying he had just been in charge of checking the lists of deportees and monitoring the actions of Soviet state security bodies and local authorities.
Meri received a Gold Star of the Hero of the Soviet Union during World War II. He was wounded four times during a battle in July 1941.
He was a cousin of the late former Estonian president Lennart Meri.
The lower house of Russia's parliament, the State Duma, adopted in May 2008 an address to members of the European parliament demanding a halt to the 'shameful trial' of the 88-year-old Soviet war hero.
"The trial is a purely political order to revise the results of WWII and to discredit the efforts of the anti-Hitler coalition to save mankind from the fascist plague," the statement read.
While Russia maintains that the Red Army liberated the Baltic states of Latvia, Lithuania and Estonia from Nazi invaders, many local residents fail to distinguish between the Nazis and the ensuing Soviet period.