Vytaustas Makauskas, spokesman for the department, said the Kavkazcenter site had been closed over the weekend using "technical means."
"It is a temporary action, the final decision will be taken after a court judgment," he added.
The decision was taken at a meeting of Lithuania's state defense council, whose members are the president, parliamentary speaker, defense minister, and army chief.
Prime Minister Algirdas Brazauskas said after the meeting that the site instigated religious and national hatred, which is forbidden under Lithuanian law.
Chechen warlord Shamil Basayev, on September 17, claimed responsibility for the deadly school hostage-taking in a letter posted on kavkazcenter.com, which is operated from a private apartment in the capital Vilnius.
Founded in 1990, kavkazcenter.com has regularly been used by Basayev and other hardline Chechens.
It also has occasionally published statements by former Chechen president Aslan Maskhadov.

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