A representative of Open Russia said the charity will appeal the ruling to Russia's Constitutional Court and, if it fails there, to the European Court of Human Rights in Strasbourg.
Open Russia's bank accounts were seized March 16 as part of a probe into the past activities of Khodorkovsky and his business partner, Platon Lebedev.
Both men are serving eight-year jail sentences -- Khodorkovsky in eastern Siberia and Lebedev in the Russian Far North -- for tax fraud and embezzlement, crimes they deny committing.
Before its bank accounts were seized, Open Russia funded educational, social, and rights advocacy programs in many Russian regions.
(Interfax, ITAR-TASS)