Estonia announced the expulsion of 21 Russian diplomats and embassy staff in order to "reach parity" between the two nations' diplomatic personnel on Wednesday.
Tensions between Russia and its European neighbors have spiked since Moscow invaded Ukraine last year.
The number of positions at Russia's embassy in Tallinn and Estonia's diplomatic mission in Moscow would now be equal, the foreign ministry added.
The expelled individuals have been given until the end of the month to leave Estonia.
"There are no grounds for the current size of the Russian embassy," Estonian Foreign Minister Urmas Reinsalu said.
The Russian embassy in Tallinn will be reduced to eight diplomatic positions and 15 administrative, technical, and service staff members.
Last April, Russia ordered the Estonian consulates in St. Petersburg and the western Russian city of Pskov to close and declared their staff persona non grata.
Moscow took the decision in a tit-for-tat move after Estonia joined its Baltic neighbors Latvia and Lithuania in expelling Russian diplomats over Moscow's invasion of Ukraine.