Alexander Kuchma requested 500,000 rubles ($14,000) in compensation over an alleged homosexual incident involving Khodorkovsky, sentenced to eight years in prison in 2005 for fraud and tax evasion. The subject of the claim is supposed to have taken place three years ago.
Lawyer Natalya Terekhova told journalists after the verdict was read that the claim was most likely initiated by penitentiary authorities, adding that neither Khodorkovsky nor his lawyers admit the claim "as the circumstance indicated in the claim just did not take place."
Khodorkovsky's lawyers presented documents saying Kuchma is undergoing psychiatric treatment.
The Moscow City Court said Tuesday that Khodorkovsky and his former business partner had been brought from jail in East Siberia to Moscow for court hearings on new charges against them.
Khodorkovsky, 45, and Platon Lebedev, 42, are already serving eight-year sentences for tax evasion and theft charges. Many critics say the charges were politically motivated.
The new charges against them include the embezzlement of more than 890 billion rubles ($25 billion at current exchange rates) and money laundering of 487.4 billion rubles and $7.5 billion.
Preliminary hearings in the new case are due to start on March 3.
Once Russia's largest oil producer, Yukos collapsed after charges of tax evasion led to the company being broken up and sold off to meet debts. The bulk of the company's assets were bought up by state-run oil company Rosneft and it was declared bankrupt in 2006.