Khodorkovsky, once Russia's richest man, is serving a 13-year sentence near the Arctic circle on charges of multi-million dollar tax evasion and money laundering. It was not immediately clear if Thursday's ruling could be overturned on appeal.
His Yukos oil company was broken up and sold off, mainly into state hands, after his arrest in 2003. Khodorkovsky, who is now 49, had appeared to defy calls by the president for rich businessmen, or oligarchs, not to get involved in politics.
Putin once dismissed Khodorkovsky's case by saying thieves must sit in jail. But asked about the ruling on Thursday, he said he bore no grudge against him and said he had not played any role in the court's decision.
"As for Mikhail Borisovich (Khodorkovsky), there was no personal persecution. This is a purely an economic crime. The court took its decision," Putin told his annual news conference.
"As regards my opinion that a thief must sit in jail, who is against that? Should he walk the streets?," he said.
Khodorkovsky's jailing during Putin's first spell as president from 2000 until 2008 was widely criticised abroad. Kremlin critics regard the two men as political prisoners but the Kremlin denies this.
Opposition leaders have said in the past that the Kremlin would allow Khodorkovsky's release only when certain that he was no longer a political threat to Putin.
Putin says the judiciary is independent, but Khodorkovsky's imprisonment was interpreted by the former KGB spy's opponents as a warning to wealthy tycoons to stay out of politics. It was also seen as the beginning of a Kremlin drive to increase state control over lucrative oil investments.
The two men have waged court battles for years against their sentences, both in Russia and in the European Court of Human Rights. In the latest appeal, their lawyers based their cases on changes to Russian criminal law.
Defence lawyer Vadim Klyuvgant welcomed the ruling as "a little human relief" in comments published on Khodorkovsky's website, but said it was deliberately timed to coincide with Putin's nationally televised annual news conference.
Khodorkovsky is one of the tycoons who made huge fortunes following the collapse of the Soviet Union in 1991. He says he has been prosecuted over business practises that were both legal and widely used.
Lebedev and Khodorkovsky have hoped repeatedly to secure early release but their hopes have been dashed on each previous occasion.
Lebedev's defence lawyers had earlier persuaded a court to reduce his prison term by three years and four months, but a higher court struck down the ruling.
The lower court then cut Lebedev's term by three years, only for the higher court to reject that decision too.
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