The Russian Foreign Ministry said that Moscow declared Estonian Consul General in St. Petersburg and the Consulate General's Pskov chancellery head persona non grata.
The expelled Estonian diplomats should leave Russia within five days.
Commenting on the decision, the ministry said that the "destructive path" chosen by Estonian authorities will affect bilateral ties with Russia, adding that Tallinn is responsible for the consequences.
Last week, Estonian authorities sent a note to Russian Consul General in Narva Dmitry Kazennov and Senior Consul Andrei Surgaev demanding their expulsion from the country. The reasons for such a decision remain unknown.
The Russian Foreign Ministry called the move "provocative and unjustified," adding that Moscow will respond.
Russian Ambassador to Estonia Alexander Petrov said last Friday that the expelled employees had done a lot to improve the bilateral relations.