"Preliminary investigations established that the defendants, being members of an organized group which included main Yukos shareholders, misappropriated stocks belonging to the Eastern Oil Company from November 6 to June 12, 1998, worth 3.6 million rubles," the Russian Prosecutor General's office said.
The charges also include expropriating oil, and laundering $25 billion earned from oil sales in 1998-2004. Khodorkovsky and Lebedev, already serving an eight-year prison term, have denied the allegations.
Now that the formal indictment had been determined the case should now be referred to a court.
A defense lawyer, Vadim Kluvgant, said that the defense had no idea which court would hear the case.
"The copy of this 'masterpiece' [the bill of indictment] was handed to the defendants yesterday in Chita," he said. "We have yet to study the content."
Khodorkovsky, 45, and Lebedev, 41, were found guilty of tax evasion and large-scale fraud by a Moscow court in May 2005 and sentenced to nine years in prison. The Moscow City Court later reduced their terms to eight years.
The jailing of Khodorkovsky and other executives of what was once Russia's largest independent oil producer has been widely criticized in the West and seen as part of the Kremlin's drive to regain lucrative energy assets.