Slovakia is to expel three staff from the Russian embassy in the capital, Bratislava, with local media reporting it is related to the murder of a Georgian man in Berlin last year.
Authorities cited the abuse of Slovak visas for the expulsions.
Germany has accused Russia of ordering the murder of the former Chechen rebel Zelimkhan Khangoshvili.
The 40-year-old was shot dead in broad daylight last August in Berlin's Kleiner Tiergarten park.
A Russian national identified as Vadim K has been charged with the murder.
Why are the diplomats being expelled?
“According to information from the Slovak intelligence services, their activities were in contradiction with the Vienna convention on diplomatic relations,” a Slovak foreign ministry spokesman said.
“On the top of that, there had been an abuse of visas issued at the Slovak general consulate in St Petersburg, and in this connection a serious crime was committed on the territory of another EU and NATO member state,” he said.
Local media, as well as investigative website bellingcat.com, have reported that one of those suspected of planning the murder had travelled to the EU on a Slovak visa.
All three must leave the country by 13 August.