Bratislava had expelled three Russian officials earlier this month for alleged diplomatic violations.
ADVERTISEMENTRussia says it has expelled three Slovakian diplomats in response to a similar move by Bratislava earlier this month.
Bratislava had ordered three Russian diplomats to leave the country on March 14 for violating the "Vienna Convention on Diplomatic Relations".
Slovakia's foreign ministry had said the decision was made after officials had assessed information from the country’s intelligence services.
Russia had said it would respond to the "unjustified" expulsions, which came amid tensions over the invasion of Ukraine on 24 February.
Slovakian Ambassador Ľubomír Rehák was summoned to the Russian foreign ministry on Monday and was informed of Moscow's decision.
"In retaliation for the expulsion in March this year, [the Russian foreign ministry] decided to declare three diplomats of the Embassy of the Slovak Republic in Moscow 'persona non grata'," a statement read.
"They were ordered to leave the territory of Russia within 72 hours," it added.
Moscow said it had also "strongly protested" against obstructing the work of Russian diplomatic missions in Slovakia and "threats to their safe functioning".
"The Ambassador was firmly warned against the recent increase in vandalism of memorials and gravesites of Soviet soldiers in Slovakia," the ministry added.