The former chief of the Yukos oil giant was brought from Moscow's Matrosskaya Tishina prison, where he has spent the last seven months since his arrest.
The hearing was adjourned till next week, and no date was set for the start of what will be Russia's highest-profile fraud trial.
Khodorkovskii faces trial on seven counts, including fraud and tax evasion running to more than $1 billion, and could go to jail for 10 years if found guilty.
The Council of Europe official said she was not satisfied after being denied access to Khodorkovskii and Lebedev.
His supporters say the case is politically motivated and meant to punish him for supporting opponents of President Vladimir Putin ahead of last year's parliamentary elections. That's denied by the Kremlin, which says the probe is part of its battle against corruption.
The case is also seen as sending a signal to Russia's other oligarchs -- the tycoons who amassed vast wealth in often shady privatization deals in the 1990s -- to stay out of politics.
Aside from Khodorkovskii, two other tycoons have also fallen out of favor with the Kremlin. Boris Berezovskii and Vladimir Gusinskii both held media interests that questioned the Kremlin's rule. They have since battled fraud charges from exile, after leaving Russia as Putin came to power.
This week, Putin made no mention of the Yukos affair in his annual address to both chambers of the legislature. But he made what many interpreted as a veiled reference to groups funded by organizations like Khodorkovskii's Open Russia Foundation charity.
"But not all [nongovernmental organizations] are intent on defending the real interests of the people," he said. "Some of these organizations are more interested in receiving funding from powerful foreign and domestic funds, or in serving suspicious group and commercial interests."
Today's hearing comes after an envoy from Europe's top human-rights watchdog was in Moscow to study the prosecutors' probe into Yukos.
Sabine Leutheusser-Schnarrenberger, from the Council of Europe's Parliamentary Assembly, said she will report in the autumn on possible human rights and legal violations in Khodorkovskii's prosecution. And she said she was not satisfied after being denied access to Khodorkovskii, Yukos shareholder Platon Lebedev, and security head Aleksei Pichugin, who are all in custody. "The judge of the Meshanski Court of Moscow who is dealing with this case told me that he cannot give me permission to visit the defendants because it is not allowed under Russian legislation," she said.
Khodorkovskii's prosecution is just one part of a legal onslaught against Yukos, which has seen its shares slump by nearly one half.
This week, a court ordered the firm to pay $3.5 billion in back taxes, a move Yukos said could force it to declare bankruptcy this year.
Khodorkovskii and Lebedev are being held on similar charges. Lebedev's lawyer, Yevgenii Baru, told RFE/RL's Russian Service yesterday the two men should be tried together. "This is about individuals who are charged with the same crimes, at the same time, under similar circumstances," he said. "Both Khodorkovskii and Lebedev are equally interested in having the cases against them disproved. So the defense feels that joint knowledge, joint efforts will help both defendants fight the criticisms and accusations in a dignified manner, and in this way, will help get to the truth in the trial."
A separate hearing in Lebedev's trial is scheduled for later today.
(RFE/RL's Russian Service contributed to this report.)