"We can confirm that Estonia has expelled two Russian diplomats," ministry spokeswoman Sandra Kamilova told AFP.
The incident follows a string of spy cases. Most recently, a Tallinn court earlier this month sentenced a Russian citizen living in Estonia to five years behind bars for spying on behalf of Russia's GRU military intelligence agency.
The Baltic News Service named the two men as Dmitry Kazennov, the Russia's consul general in the eastern city of Narva and consul Andrey Surgaev.
Relations between Moscow and Tallinn have been fraught since Estonia broke free from the crumbling Soviet Union in 1991, joining both the EU and NATO in 2004.
NATO is currently deploying four battalions to the three Baltic states - Estonia, Latvia and Lithuania - and Poland to reassure its allies spooked by Russia's frequent military exercises near the region and its 2014 annexation of Crimea from Ukraine.