Yury Shmidt's comments came amid press speculation that the new trial of Khodorkovsky and business partner Platon Lebedev may open before the March presidential election.
Khodorkovsky and Lebedev were convicted in 2005 of fraud and tax evasion and sentenced to eight years in prison in a case that many critics called Kremlin revenge for his criticism and apparent political ambitions.
Prosecutors last year announced new charges of embezzlement and money laundering against the two.
Nearly a year later, "the question that upsets us the most is where the case will be heard and when," Shmidt said at a news conference. "To both these questions, I answer, 'I don't know.'"
If convicted on the new charges. Khodorkovsky and Lebedev could be sentenced to 22 1/2 years each, he said.
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