It did not name those to be expelled, but said the decision followed Moldova's decision on Monday to expel five Russian diplomats.
A spokeswoman for the Moldovan Foreign Ministry announced the initial expulsions on Tuesday without disclosing a reason.
As per reports, the expelled Estonian diplomats have been asked to leave Russian Federation within five days.
"I am deeply outraged by this unfriendly step".
The foreign ministry in Moscow said it was giving Estonia's consul in the second city of Saint Petersburg and another diplomat in the city of Pskov five days to quit the country.
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Moldovan President Igor Dodon told Sputnik that he condemned the move taken by the Moldovan government.
Russian Foreign Ministry said Nikolae Miinea, the Minister-Counselor of the Moldovan Embassy, was invited to the ministry, where a note was given to him.
TASS earlier reported citing Russian Ambassador to Estonia Alexander Petrov that Russian Consul-General in Narva Dmitry Kazennov and Consul Andrei Surgayev will leave Estonian on the demand of the local authorities until the end of this month.
"The continuing destructive policy of the Estonian authorities will inevitably have the most negative impact on bilateral relations".
Moldova, one of the poorest countries in Europe, has been torn between integration with the European Union and loyalties to its former Soviet ruler, Moscow.