"Today the suspects will be questioned in the presence of their lawyers," the Main Investigation Committee of the Prosecutor General's Office said in a news release on Tuesday.
Khodorkovsky, who turned 45 on June 25, 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 two men are currently serving their sentences in East Siberia. Both men have maintained they are innocent of the charges, with Khodorkovsky claiming the sentence was retaliation for his support of Russia's tiny opposition movement.
Defense lawyers called the new charges on Monday "an assortment of absurd and groundless allegations relating to the theft and legalization of the entire volume of oil produced by the Yukos oil company over a six-year period."
The new charges were pressed shortly after Khodorkovsky's defense announced that they had prepared a parole application for their client.
The Russian daily Vedomosti reported last week that Khodorkovsky could be freed next year if Russia's parliament approves a bill to review sentencing as part of a move to cut the prison population.
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.