Speaking during a new trial in Moscow, Khodorkovsky said investigators had "worded the accusations in vague and misleading terms, used deliberately contradictory and untrue statements that discredit me and are unrelated to the article of the Criminal Code I am accused under."
State prosecutor Valery Lakhtin dismissed Khodorkovsky's claims on Tuesday, saying the charges had been explained.
"Their [the suspects'] behavior in the courtroom has disproved their claims that the charges are unclear," Lakhtin said.
Khodorkovsky and his business partner Platon Lebedev, who are already serving eight-year sentences for fraud and tax evasion, are facing fresh embezzlement and money laundering charges totaling about $50 billion, which could see their jail terms extended by 21 years.
Defense lawyers acting for the businessmen have called their clients political prisoners, and say the new charges are "disgraceful" and unsubstantiated.
Khodorkovsky said investigators had refused to lay out the charges, which was part of a conspiracy to have him jailed for a longer term.
"State prosecutors have demonstrated unwillingness to carry out an honest investigation and now a trial," the businessman said, insisting on explanations on the charges.
Lakhtin said prosecutors had been unable to read out the indictment for the three days of the hearings as Khodorkovsky and Lebedev and their lawyers had kept filing appeals.
Khodorkovsky and Lebedev, who have pleaded innocent on both sets of charges, are now in a Moscow detention center after being transferred from a Siberian prison, where they have been serving their sentences since 2006.