The defense said it wants a second case against their clients, being presided over by Khamovniki Court judge Viktor Danilkin, removed from the trial.
Khodorkovsky's lawyer, Natalya Terekhova, said the case came to the Khamovniki District Court with an accompanying letter indicating that it should be considered by Danilkin.
"That is why we believe he will not be unbiased, as a judge must be," she said.
Preliminary hearings on new charges against Yukos founder Khodorkovsky, and Lebedev, started in Moscow on Tuesday.
Two Russian oil companies, Tomskneft and Samaraneftegaz, have filed a new 170 billion ruble ($4.7 billion) suit against Khodorkovsky and Lebedev.
Khodorkovsky, 45, and 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 the current rate of exchange) and laundering of 487.4 billion rubles and $7.5 billion.
They now face total claims of about $50 billion, which their lawyers have described as "ridiculous."
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.
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