Lebedev, who also pleaded not guilty, condemned the conduct of the case.
He said: "This is not an accusation but a schizophrenic fraud... I have never stolen anything nor raided anything in my life, either individually or in a group.
"To confess to a crime that has not taken place is ridiculous."
Khodorkovsky, previously Russia's richest man and the former head of the now disbanded Yukos oil company, was sentenced to eight years in prison on fraud and tax evasion charges four years ago.
His supporters have condemned the trial against him as politically motivated and say it is aimed at keeping Khodorkovsky, a critic of Vladimir Putin, Russia's prime minister, out of the political scene indefinitely.
Khodorkovsky, 45, is said to have irritated the Kremlin by openly funding opposition political parties.
The former businessman has said he is the victim of corrupt officials who feared his political ambitions and wanted to carve up his business empire.
In a separate development, a district court judge in Moscow ordered the release on parole of Svetlana Bakhmina, a former lawyer for Yukos, who was serving a six-and-a-half year prison term on embezzlement and tax evasion charges.
Bakhmina gave birth to a child in November, after being transferred to a detention centre near Moscow.
Human rights activists had protested against her imprisonment at the time, saying it was inhumane to keep a pregnant woman in jail.
Irina Vyrysheva, the judge, said: "Bakhmina has shown she is eager to reform, she is no longer a threat to society and does not need to continue serving her term.
"The court rules to satisfy the plea of the convict regarding her early release."