Khodorkovsky and Lebedev pleaded not guilty to all charges against them during the trial in Moscow last Tuesday.
The two men, who have been serving eight-year sentences for fraud and tax evasion since 2005, were transferred from a Siberian prison to a Moscow detention center in February for the trial on the fresh embezzlement and money laundering charges.
The defendants' lawyers argued the case contained numerous technical errors and inaccuracies.
Prosecutors earlier admitted there were some mistakes in the indictment, but said they would not influence the trial.
Prosecutor Dmitry Shokhin asked the court to reject the plea as "lacking in merit."
He argued that the defense had filed the motion just to drag out the judicial process.
The new charges against Khodorkovsky and Lebedev involve the theft of government shares and the laundering of money earned from illegal oil sales, in total worth about $50 billion. If convicted, the two could see their jail terms extended by 20 years or more.
Lawyers acting for the businessmen have called their clients political prisoners, and say the new charges are "disgraceful" and unsubstantiated.