The Strasbourg-based court, which considered Khodorkovsky's case together with that of his business partner Platon Lebedev, ruled that the tax-fraud accusations against them had a "healthy core," and "corresponded to a common-sense understanding of tax evasion."
On July 25, the court released its findings on a series of complaints filed earlier by the two men.
The ruling said that Russia unfairly charged Khodorkovsky huge tax arrears, and that he and Lebedev were unjustly sent to serve their sentences in penal colonies in eastern Siberia, thousands of miles from their families.
But the ECHR found no basis that the case against the two was politically motivated, as Khodorkovsky and Lebedev alleged in their complaint.
In its findings, the court said that "some government officials had their own reasons to push for the applicants' prosecution," but it added that it was "insufficient to conclude that the applicants would not have been convicted otherwise."
The court said there was no violation of the defendants' right to a fair trial in terms of the impartiality of the judge, but mentioned violations of lawyer-client confidentiality and the unfair taking and examination of evidence by the trial court.
The court agreed with Lebedev's complaint that his confinement in a metal cage during court proceedings amounted to humiliation.
The rights of defendants are contained in the European Convention on Human Rights.
Khodorkovsky was arrested in 2003 and later convicted of tax fraud and sentenced to nine years in prison.
His company Yukos Oil was hit with a series of tax claims from the Russian government that totaled some $27 billion and later dismantled.
In 2010, Khodorkovsky was convicted in a second case of stealing oil from his own company.
Lebedev is now due to be released in August 2014, and Khodorkovsky in October 2014.
The defendants' lawyers criticized the ruling.
Karinna Moskalenko, a lawyer for Khodorkovsky, expressed disappointment with the ECHR decision.
"First and foremost -- the fundamental right to a fair trial was violated," she said. "And that, in accordance with Russian law, requires that the convictions be overturned."
Vladimir Krasnov, a lawyer for Platon Lebedev, said he found it "a bit strange" that the ECHR could not determine the political nature of the accusations against Khodorkovsky and Lebedev.
"I am, to a certain extent, disappointed with this part of the ruling," he added.
Khodorkovsy's mother, Marina, criticized the ruling in a message on the Internet, describing it as "cowardly and perhaps incompetent." She added that "only a blind, deaf, and dumb person would not be able to see the political motives behind everything that has happened to Yukos."
The ECHR ruling on July 25 ordered Russia to pay Khodorkovsky 10,000 euros ($13,000) in damages.
In spite of the fine, Russian news agency ITAR-TASS quoted sources from the Justice Ministry as saying they were "satisfied" with the ECHR conclusion that the trial had not been politically motivated.