Deputy general prosecutor Alexander Zvyagintsev told the Interfax news agency in an interview that Khodorkovsky was unlikely to benefit from a planned presidential amnesty this year.
"There are several criminal cases under investigation involving him and several other people, which have a good chance of making it to trial," said Zvyagintsev, Interfax reported.
Zvyagintsev appeared to indicate that it was highly unlikely that Khodorkovsky, who has been convicted of tax evasion and embezzlement in two highly controversial trials, will have a chance for the amnesty now mooted in the Kremlin.
He gave no indications on the nature of the other cases. Usually, the opening of criminal cases over serious crimes is announced by Russia's Investigative Committee, its equivalent of the FBI.
Once Russia's richest man, 50-year-old Khodorkovsky was arrested in October 2003 and convicted of fraud and tax evasion two years later. A second trial ended in 2010 with an embezzlement conviction.
He is due to be released in August 2014.
President Vladimir Putin said this week that the amnesty would not include people who committed "serious crimes".
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