Vandals desecrated buildings belonging to the Lithuanian Jewish minority in the town of Panevezys and the capital, Vilnius, local media reported on Monday.
Unknown people sprayed swastikas and offensive words on the buildings over the weekend, including a wall of the Jewish community centre in Vilnius. Someone had spray-painted "Juden Raus" on the building, reminiscent of the neo-Nazi rally in the Lithuanian capital earlier this year, dpa reported.
The police launched an investigation. President Valdas Adamkus condemned the acts.
"Humiliation of people who suffered in the Holocaust is not mere hooliganism," Adamkus was quoted as saying by the ru.delfi.lt website on Monday.
"It is a destructive and despicable act, aimed not only against the Jewish community in Lithuania, but also against Lithuania itself."
In recent months, public attention has been turned to Jewish issues in the small Baltic nation that joined the EU and NATO in 2004, including construction on the site of the Jewish cemetery in Vilnius, restitution of property which belonged to the Jews before World War II and a government investigation into the wartime activities of the former Jewish partisans.