Gen. Sergei Shoigu, Russian defense minister, was accused by the Ukrainian Internal Affairs Ministry of involvement in forming "illegal military groups" in eastern Ukraine, led by Russian citizens, that "make regular attacks on government institutions and other organizations that have led to multiple human deaths, destruction, and other consequences," a statement said.
Russian billionaire and investment fund founder Konstantin Malofeev was also indicted, accused of financing "illegal military units." He has denied any role in the uprising, although it had been reported the self-styled leader of the "Donetsk People's Republic" was formerly a Malofeev employee.
A criminal case was begun earlier in July against the chief of Russia's border service.
The ministry statement did not mention the crash of Malaysia Airlines Flight 17, believed to have been downed July 17 by missile fire of the pro-Russian separatists in eastern Ukraine.