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.
“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.
Russia has said it will respond, but did not give any further details.
In December, Germany expelled two Russian diplomats due to suspicions the Kremlin was involved in the murder. Russia responded by expelling two German diplomats.
In June, Germany’s federal prosecutor said Vadim K took the “government order to kill” in the hope of financial reward or because he shared the desire to “kill a political opponent”.
Prosecutors say in August 2019 Vadim K flew from Moscow to Paris and from there to Warsaw, before arriving in Berlin, using a passport under the name Vadim S issued by Russian authorities just a month previously.
On 23 August he allegedly came up behind Khangoshvili on a bicycle and fired a shot into his torso using a silenced Glock 26 pistol. Prosecutors say he then fired two more shots into the victim’s head as he lay on the ground, killing him.
Vadim K was arrested shortly afterwards and has been in pre-trial detention since.
Russia has previously called accusations it was involved in the crime “absolutely groundless” and said it had nothing to do with the death.
Zelimkhan Khangoshvili was a Georgian citizen of Chechen descent and had reportedly been an asylum-seeker in Germany since 2016.
He had fought against Russia as the leader of a Chechen militia between 2000 and 2004, and also put together a group of volunteers to defend the enclave of South Ossetia in 2008 on behalf of the Georgian government – although they were never deployed.
Germany’s federal prosecutor said Russia had accused him of being a terrorist.