Khodorkovsky, the former head of Yukos, and business partner Platon Lebedev were convicted by a Moscow court of embezzlement and money laundering. They already are serving prison terms for tax evasion.
"We are troubled by the allegations of serious due process violations, and what appears to be an abusive use of the legal system for improper ends," a statement issued by the White House press office said. "The apparent selective application of the law to these individuals undermines Russia's reputation as a country committed to deepening the rule of law."
Secretary of State Hillary Clinton echoed the White House statement, saying the case and others like it "have a negative impact on Russia's reputation for fulfilling its international human rights obligations and improving its investment climate."
The White House warned failing to keep a "commitment to universal values … impedes its (Russia's) own modernization and ability to deepen its ties with the United States."
The statement said U.S. President Barack Obama and Russian President Dmitry Medvedev have discussed the case and the Russian leader has pledged to "strengthen the rule of law."
RIA Novosti reported the Khamovniki court ruled Khodorkovsky and Lebedev led an organized group committing financial crimes through their Yukos oil company and used embezzled funds for their own enrichment.
The court also ruled Yukos had signed fake agreements with its subsidiaries on the purchase of oil, buying oil products from them at prices that were half or a quarter of the average.