Russia on Friday declared 18 diplomats of the EU office in Moscow persona non grata.
Prior to the retaliatory move, the Foreign Ministry summoned EU ambassador Marcus Exeter and expressed its strong protest against the expulsion of 19 Russian diplomats from the country's office to the EU.
"The Russian side has declared the EU's responsibility for the consistent destruction of the architecture of bilateral dialogue and cooperation that has been created for decades," the ministry said in a statement.
It also told Exeter of the need for Brussels to comply with the 1961 Vienna Convention on Diplomatic Relations, the statement added.
Soon after the move, EU foreign policy chief Josep Borrell said the bloc "deplores the unjustified, baseless decision" by Moscow.
In a statement, Borrell asserted that the EU diplomats were fulfilling their duties "in the framework of and in full respect for the Vienna Convention on Diplomatic Relations."
"There are no grounds for Friday’s decision by the Russian authorities beyond being a pure retaliatory step," he added.
Calling on Russia to stop its aggression against Ukraine, he said: "Russia's chosen course of action will further deepen its international isolation."
At least 1,982 civilians have been killed and 2,651 injured in Ukraine since the war began on Feb. 24, according to UN estimates, with the true figure believed to be much higher.
Nearly 4.8 million Ukrainians have fled to other countries so far, with over 7 million more internally displaced, said the UN refugee agency.