The ministry barred entry for foreign nationals coming from Croatia, citing the worsening coronavirus situation in the country.
The travel ban currently also applies to Luxembourg, Sweden, Portugal, Belarus and Romania.
Lithuanians arriving from Ukraine will no longer be subject to a mandatory 14-day quarantine as of Monday, according to the ministry's press release.
Travelers from Iceland and Spain will be advised to go into isolation, it said.
The list of coronavirus-affected countries is updated every week based on the epidemiological situation.