The recently discovered remains of five soldiers from the Nazi 20th SS division were to be reburied alongside members of the Estonian rifle corps, who fought on the Soviet side. All of the men perished during the Battle of Porkuni on September 21, 1944. The battle, in which around 500 men lost their lives, was the largest to be fought in Estonia during WWII.
The ceremony comes just a day before Estonia is due to celebrate the Day of Resistance, renamed last March from the Day of Tallinn's Liberation from Nazi Occupation.
Russian-Estonian relations hit a new low in May after Estonian authorities dismantled a Soviet-era war monument, the Bronze Soldier, and disinterred the remains of Soviet soldiers ahead of May 9, celebrated as Victory Day in Russia.
This provoked mass protests in Tallinn and other Estonian cities, during which over 1,000 people were detained, dozens injured and an ethnic Russian killed. Rallies, including a blockade of the Estonian embassy organized by the pro-Kremlin youth group Nashi, also took place in Moscow.
The issue of monuments to Soviet soldiers in Estonia has long been a controversial one in the Baltic country of 1.3 million people. Many Estonians see no difference between the periods of Nazi and Soviet occupation, and resent Soviet-era statues dedicated to the country's 'liberators'.
Estonia was occupied by Nazi forces from 1941-44 and by the Soviet Union from 1941-1991.
In March, Estonia's President Toomas Ilves vetoed on technical grounds part of an act that obliged the government to demolish Soviet war memorials within 30 days.