Khodorkovsky, who was once Russia's richest man, was sentenced to an eight-year term in 2005 and has been eligible for parole for the past 10 months.
His lawyers said that the early release hearing was a test case for new Dmitry Medvedev, Russia's new president, who has said he wants to improve the rule of law and end arbitrary legal decisions.
Yuri Schmidt, Khodorkovsky's lawyer, immediately announced that he would challenge the ruling, the Interfax news agency reported.
Khodorkovsky maintains that the charges against him were politically motivated and initiated by Vladimir Putin, Medvedev's predecessor and current prime minister, who feared his political ambitions.
In June, new charges of embezzlement and money laundering were brought against the former Yukos boss and Platon Lebedev, his business associate.
Khodorkovsky said in a newspaper interview on Friday that if freed he would not return to the oil business and would not mount any legal battle for his former Yukos company.
"I have already told the court that I am not prepared to return to the oil business and will not seek to overturn unfair decisions concerning Yukos," he told the Vedomosti newspaper.
The charges against the Kremlin critic, and subsequent demand for huge back taxes from Yukos, led to the effective renationalisation of the oil giant, which was taken over by the state oil company Rosneft.