EUROPE'S rights court says the trial of anti-Kremlin tycoon Mikhail Khodorkovsky, one of Russia's most high-profile prisoners, has been "unfair" and ordered Moscow to pay compensation.

But the European Court of Human Rights also concluded that the judge who presided over the 2005 proceedings against Khodorkovsky, now 50, and his business partner Platon Lebedev, 56, had been impartial.

Khodorkovsky's supporters have long accused the court of being biased and the trial politically motivated.

"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 on Thursday.

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.

He was convicted of large-scale tax evasion in 2005, along with co-accused Lebedev, following his dramatic arrest at a Siberian airport two years earlier.

In 2010, both men received fresh convictions for fraud, extending their prison sentences until 2016, although Khodorkovsky's sentence has since been reduced by two years.

Thursday's ruling -- which only applies to the 2005 trial -- is the court's second judgment on the controversial case.

The court - based in the eastern French city of Strasbourg - had already ruled in 2011 that the prosecution of Khodorkovsky was not politically motivated.

In Thursday's ruling, it repeated this assertion but nevertheless found several breaches of the European Convention on Human Rights.

These included breaches of the right to a fair trial with regards to "lawyer-client confidentiality and the unfair taking and examination of evidence by the trial court."

The court also said there had been a violation of the right to respect for private and family life after both men were transferred to penal colonies in Siberia, "several thousand kilometres away from Moscow and their families."

The court also found 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."

The court ordered Russia to pay 10,000 euros ($A14,503.26) to Khodorkovsky, while damage payments demanded by Lebedev "were rejected in full."

Khodorkovsky's supporters have long argued he is innocent of the financial crimes and claimed the charges against him were ordered by the Kremlin to eliminate a potentially dangerous political opponent.