"Charges against two Russian business executives (Khodorkovsky and Lebedev) had a sound basis, but the hearing of their case was unfair, and their placement in remote penal colonies unjustified," the court ruled.
Khodorkovsky, the high-profile former boss of oil giant Yukos and once Russia's richest man, has spent the last decade behind bars on charges of financial crimes that supporters say were politically motivated.
He was convicted of large-scale tax evasion and fraud in 2005 along with co-accused Lebedev following his dramatic arrest at a Siberian airport in 2003.
These include breaches of the right to a fair trial with regards to "lawyer-client confidentiality".
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The court also noted that Khodorkovsky's lawyers had been harassed by authorities.
It however found no violations "with regard to the impartiality of the judge who presided at the applicants' trial or with regard to the time and facilities given for the preparation of their defence.