Anna Usachyova said that both men need to appear at Moscow's Khamovniki District Court to be indicted on the new charges, adding that the hearings on the second criminal case against them would start on March 3.
She added that the preliminary hearings, in accordance with the law, would take place behind closed doors.
Khodorkovsky, 45, and Lebedev, 41, were found guilty of tax evasion and grand theft 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 new charges include embezzlement of more than 890 billion rubles ($25 billion at the current rate of exchange) and laundering 487.4 billion rubles and $7.5 billion.
A federal prison official previously said a second trial against Khodorkovsky could go ahead without him having to appear in the courtroom as it could be held via video conference.
However, a Khodorkovsky lawyer said on Wednesday a court hearing without the defendant physically being present would be illegal.
Yury Shmidt said in this case he would advise his client to refuse to participate in such a hearing and that the defense would also refuse.
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.