Russia has begun repair works on rail links with Estonia, reducing oil transit through the country. Deliveries of coal have also been affected.
The Estonian government accuses Russia of blocking trade for political ends in the two countries' spat over the recent removal of a World War II memorial from central Tallinn.
The European Commission also described as "inaccurate" reports that the European Union is considering blocking Russia's entry into the World Trade Organization (WTO) over multiplying bilateral disputes.
Spokesman Peter Power said in Brussels that Russia's WTO entry is in both Russia's and the EU's interest, as it would encourage reforms and provide a better framework for resolving trade disputes.
He said that a "small number" of problems remain before the EU can give its final green light.
Meanwhile, around 300 activists of a pro-Kremlin youth group, Nashi, rallied outside the Moscow offices of the European Commission's delegation to Russia demanding the release of a fellow teenage activist arrested in Tallinn.
The activist was arrested for organizing protests against the removal of the war memorial in Tallinn. On May 3, Nashi ended a weeklong protest outside the Estonian Embassy in Moscow against the memorial's removal.
(compiled from agency reports)