The NGO had lodged an appeal against a Basmanny Court order on March 22 to freeze 200,000 rubles ($7,300) on Open Russia's accounts.
Last week, Moscow City Court rejected an appeal by the NGO against a Basmanny Court decision on March 16 to freeze $5.5 million on Open Russia's accounts at Moscow-based National Bank Trust, following a request from the Prosecutor General's Office.
Investigators said funds in the accounts were of illegal origin and belonged to suspects in criminal cases related to Khodorkovsky, the former CEO of embattled oil company Yukos, and his business partner and former Group Menatep director Platon Lebedev.
Khodorkovsky and Lebedev are both serving eight-year prison terms for money laundering and tax evasion.
Open Russia said its funds were absolutely legal and were earmarked for educational, cultural and charity projects in almost 40 regions of Russia. It said the court had violated its constitutionally guaranteed right to freely own, use and dispose of its property, and that it would appeal the decision in Russia's Constitutional Court and in the European Court of Human Rights in Strasbourg.