In a statement, Open Russia said that its bank accounts were frozen "without any explanation" after officials visited the Trast bank today.
The accounts held funds for educational, social, and rights advocacy programs in 48 of Russia's 88 regions.
Khodorkovsky, the founder and former head of the Yukos oil company, founded Open Russia in 2001.
He is serving an eight-year prison sentence for fraud and tax evasion after a trial widely seen as Kremlin-inspired punishment for his political ambitions. Yukos has been largely dismantled to pay off billions of dollars in back taxes.