The hearing took place at the IK-6 penal colony in Melekhovo, about 145 miles east of Moscow, where Navalny is already serving sentences totaling 11.5 years.
His supporters accuse Moscow of trying to break him to silence his criticism of President Vladimir Putin, something the Kremlin denies.
Journalists were not admitted to the courtroom but were able to watch a video link from a room nearby, with barely intelligible audio.
Navalny, looking thin with cropped hair and dressed in a black prison uniform, could be seen seated at a desk, leafing through papers and conferring with one of his lawyers.
He then stood and spoke for three minutes, contesting the authority of the Moscow city court judge to try him in a penal colony far from the capital.
“Taking into account the current circumstances, and criminal law, you should withdraw,” he said.
He also demanded that his parents be allowed inside the hearing, saying they had come to Melekhovo believing it would be an open session.
Soon afterward, the court adjourned for a break.
Asked for comment on the case, Kremlin spokesman Dmitry Peskov said: “We are not following this trial.”
An entry in the court record last month showed the new charges relate to six different articles of the criminal code, including inciting and financing extremist activity and creating an extremist organization.
Russia has outlawed Navalny’s campaign organization as part of a crackdown on dissent that started well before the conflict in Ukraine and has intensified in the nearly 16 months since it started. Last week one of his regional campaign leaders was jailed for 7.5 years.
In a tweet posted on his account by his supporters last month, Navalny responded with typical irony to the new charges.
“Well, Alexei, you’re in some real trouble now … The Prosecutor General’s Office has officially provided me with 3,828 pages describing all the crimes I’ve committed while already imprisoned.”
He said he had not been allowed to read the material to find out what exactly he was accused of because he was once again in solitary confinement and allowed only a mug and one book.
Navalny, 47, earned admiration from the disparate opposition for voluntarily returning to Russia in 2021 from Germany, where he had been treated for what Western laboratory tests showed was an attempt to poison him with a Soviet-era nerve agent.
The Kremlin denied trying to kill him and said there was no evidence he had been poisoned with such a toxin.
It was not immediately clear which specific actions or incidents the new charges referred to.
One relates to “rehabilitation of Nazism” — a possible reference to Navalny’s declarations of support for Ukraine, whose government Russia accuses of embodying Nazi ideology. Ukraine and its Western allies dismiss that charge as baseless.
In April, investigators formally linked Navalny supporters to the murder of Vladlen Tatarsky, a popular military blogger and supporter of Russia’s military campaign in Ukraine who was killed by a bomb in St Petersburg.
Russia’s National Anti-terrorism Committee (NAC) said Ukrainian intelligence had organized the bombing with help from Navalny’s supporters.
This appeared to be a reference to the fact that a suspect arrested over the killing once registered to take part in an anti-Kremlin voting scheme promoted by Navalny’s movement.
Navalny allies denied any connection to the killing. Ukraine attributed it to “domestic terrorism.”