The judge said Khodorkovsky was ineligible for early release from a sentence for tax evasion and fraud because he had refused to undertake professional training at his prison, which specializes in sewing, and because of an incident in which he flouted prison rules.
Khodorkovsky reacted by shaking his head as the decision was announced in the courtroom in the Siberian city of Chita.
Khodorkovsky — who headed the Yukos oil company and was once Russia's richest man — has spent almost five years in jail. He was sentenced in 2005 to an eight-year term and has been eligible for parole for the past 10 months.
Khodorkovsky's parole hearing was seen as a test of new President Dmitry Medvedev's commitment to reforming the judiciary.
The prosecution of the oligarch was widely viewed as an attempt to silence a Kremlin opponent and consolidate control over Russia's strategic energy sector.
The charges and subsequent demand for huge back taxes led to the effective renationalization of Yukos, which was taken over by the state oil company Rosneft.
Khodorkovsky also faces new charges of embezzlement and money laundering, brought in June against both the former billionaire and his business associate Platon Lebedev.