Prague has accused Russian secret agents of involvement in a deadly blast at a munitions factory in 2014.
Estonia, Latvia, and Lithuania have all expelled Russian diplomats in a show of solidarity with the Czech Republic against Moscow.
Prague has accused Russian secret agents of involvement in a deadly explosion in the country in 2014.
Czech foreign and interior minister Jan Hamacek had called on European Union and NATO member states to also kick out Russian diplomats.
On Friday, Lithuania's foreign ministry confirmed it had summoned the country's ambassador to Moscow and declared two members of the embassy "personae non-gratae".
In a statement, the ministry said the decision was taken because the two officials "had carried out activities incompatible with their diplomatic status".
"The decision shows our solidarity with the ally after an unprecedented and dangerous incident in the Czech Republic," said foreign minister Gabrielius Landsbergis.
"Lithuania fully supports the country and its actions in response to the 2014 explosions, as well as to inadequate steps taken by Russia."
The two diplomats have been given seven days to leave Lithuania, a move that could bring Russian retaliation.
Vilnius said the move was made "in close coordination" with their Baltic neighbours, Estonia and Latvia.
Estonia's foreign ministry said it had also summoned the Russian ambassador on Friday to "launch a strong protest" against information related to the 2014 blast.
"Russia has committed a grave violation of international law on the territory of a European Union and NATO member state, undermining the sovereignty of the Czech Republic," the ministry said in a statement.
"Actions of this kind are harmful to the security and stability of Europe and are unacceptable," it added.
Tallinn confirmed that they had expelled one Russian diplomat "in a show of solidarity" with Prague.
Meanwhile, Latvia said they had also declared one Russian diplomat a "persona non grata" following "illegal activities" conducted by Russia’s intelligence services in the Czech Republic.
"Latvia is interested in building a relationship with Russia on the basis of mutual respect, international law, and the principles laid down in the Vienna Convention," said Foreign Minister Edgars Rinkēvičs in a statement.
"Russia’s actions have borne evidence for an extended period of time of systemic violations of such principles and of undermining and destabilising the security situation."
Neighbouring Slovakia became the first NATO ally to show support for the Czech Republic, kicking out three Russian diplomats on Thursday.
What has caused the diplomatic dispute?
The Czech Republic has accused agents of Russia's Federal Intelligence Agency (GRU) of being behind a blast at an ammunition depot near the village of Vrbetice in 2014, which killed two people.
Last week, Czech police said they were searching for two men carrying Russian passports with the same names as the suspects in the attempted Novichok poisoning of Sergei Skripal in Salisbury in 2018. Moscow has denied the allegations
The Czech government expelled 18 Russian diplomats before Moscow retaliated by expelling 20 Czech diplomats on Monday.
Prague condemned the move by Russia as an "inappropriate reaction," saying the move had paralysed the country's embassy.
On Thursday, the Czech Foreign Ministry then confirmed that they would be ordering more Russian diplomats to leave the country, further escalating the dispute
Foreign Minister Jakub Kulhanek said Russia won't be allowed to have more diplomats in Prague than the Czechs currently have at their embassy in Moscow.
An estimated 60 more officials would have to leave the Czech Republic by the end of May, Kulhanek said.
Russian Foreign Ministry spokeswoman Maria Zakharova said the country would respond immediately again, accusing the Czech Republic of "destroying relations".
"They have gotten stuck in unbridled Russophobia," Zakharova told reporters.