However the court upheld the state's multibillion ruble tax claim against Khodorkovsky, who himself was released last month after receiving a pardon from President Vladimir Putin, the court's spokesman told AFP.
The former chief of oil Yukos firm, who left Russia immediately upon release, had said he would not be able to return as long as the tax claims against him remained in place.
The latest announcements come as the Kremlin prepares to host the Winter Olympic Games in Sochi next month.
"The main thing today is the release of Platon Lebedev," said a statement from Khodorkovsky's defence team.
"However there is bad news as well. The Presidium of the Supreme Court has not overruled the absurd claims over 17.5 billion rubles (USD 550 million)," said the statement from the defence team.
"The existence of the claim deprives Mikhail Borisovich from an opportunity to come back to Russia," the statement added.
In a move that stunned Russia, Putin last month pardoned Khodorkovsky on humanitarian grounds and the tycoon was immediately flown out of Russia.
Platon Lebedev, an associate of Khodorkovsky who was arrested in July 2003 and convicted in two highly controversial cases on charges of fraud, tax evasion, and money laundering, has been serving his sentence in the far-northern Arkhangelsk region.
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