The Russian firm’s software was banned from US government networks earlier this year amid allegations that it helped Russian intelligence steal top secret information.
“The government… recognised that Kaspersky Lab software is a potential national security threat,” the Baltic EU state’s defence ministry said in a statement.
The government agencies responsible for “critical infrastructure” must replace the popular anti-virus software in “a short while”, it added.
Lithuanian intelligence chief Darius Jauniskis recently said the cyberfirm “was sometimes acting as a toy in the hands of (Russian President Vladimir) Putin’s administration”.
Kaspersky has repeatedly denied having any inappropriate ties with the Kremlin and said that malware-infected Microsoft Office software and not its own was to blame for the hacking theft of American intelligence materials.
Kasperski told Russian media on Thursday it was “disappointed” and assured customers they “do not have to worry because they have not been subjected to any violation from our company.”
“The Kaspersky laboratory has never helped nor will it ever assist any state in the world to engage in cyber-espionage or to conduct cyber-attacks,” the company said.
“The Kaspersky laboratory has no political connection or affiliation with any government.”
Lithuania, a NATO and EU member of 2.8 million people, has been one of the most vocal critics of Russia, notably after its 2014 annexation of the Crimea peninsula from Ukraine.