"This case does not involve politics, it is solely a criminal matter," a spokeswoman for the Prosecutor General's Office told a briefing on Friday.
"Serious damage" has been inflicted on the country and its economy by the jailed businessmen's actions, she added.
Russia's top prosecutors filed new money laundering charges against Khodorkovsky and Lebedev at the beginning of the week.
Yury Shmidt, a lawyer for Khodorkovsky, said his client has been charged with embezzling and laundering $23-25 billion.
Karina Moskalenko, another lawyer for Khodorkovsky, has called the figure "completely insane."
The Prosecutor General's Office now alleges that Khodorkovsky, the founder of the now bankrupt Yukos oil company, and Lebedev are guilty of embezzling receipts from Yukos subsidiaries Fargoil and Ratibor, and of laundering the money through the Open Russia Foundation, a charitable organization established by Khodorkovsky in 2001 as a private endowment to assist academic institutions and non-governmental organizations in Russia.
Two weeks ago, Shmidt said the jailed tycoon had refused to cooperate with the investigation until he was presented with "concrete charges" and was transferred to a pre-trial detention facility in Moscow.
Khodorkovsky and Lebedev, both serving eight-year sentences in Siberia since 2005 for fraud and tax evasion, were taken to a pre-trial detention facility in Chita, in Eastern Siberia, in December 2006.
Khodorkovsky, who acquired oil assets through controversial privatization deals in the early-1990s, has insisted his case was orchestrated by the authorities to silence his criticism of President Vladimir Putin and as part of a campaign to bring mineral assets under Kremlin control.
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The main event of the third day of the 11th meeting of the Valdai International Discussion Club in Sochi was the closing session with President Vladimir Putin. The atmosphere was calm and open, despite the current political tensions and the Russia-West confrontation. The Russian president said that it corresponded to the spirit of the Valdai Club.