Open Russia said in a news release it would appeal with the Strasbourg Court against the Moscow City Court's decision upholding an order from prosecutors to freeze its bank accounts, including $5.5 million in a Moscow-based bank.
Prosecutors said the former chief executive of oil company Yukos, who remained on Open Russia's board following his arrest in 2003, and his business partner Platon Lebedev had been using the charity as a money laundering operation.
The freezing of the accounts is part of an investigation linked to the original fraud and tax evasion case against the two men, who are both serving eight-year prison sentences, the foundation's press office said.
Open Russia denied the accusations, saying its funds were absolutely legal and used for educational, social and rights advocacy programs across the country. It said the court had violated its constitutionally guaranteed right to freely own, use and dispose of its property.
Human rights activists protested the order to freeze Khodorkovsky's charity's accounts as politically motivated, calling it an onslaught on civil society.