It is yet "another gross violation of political freedoms and human rights in illegally-annexed Crimea", the ministry said in a statement on Thursday.
"It is an example of the Russian Federation's intimidation policy and attack against Crimean Tatars, aimed at suppressing the will of this nation to fight for its rights and resist the government brought in by the occupation and its policy of solidifying Crimea's annexation."
The ministry has reiterated that Lithuania does not recognize Crimea's annexation. "We deem this annexation and all institutions of the existing government and their actions illegal," the statement said.
The Republic of Crimea's prosecutor Natalia Poklonskaya has tuned to the Supreme Court of Russia, asking for the Mejlis, the self-governing body of Crimean Tatars, to be recognized as extremist organization and its activities to be banned.
Russia annexed Crimea in March 2014, sparking worldwide condemnation and leading to the European Union's decision to introduce sanctions against Moscow.
Tatars, who make up more than 12% of Crimea's population, are among the biggest critics of Moscow.