Local media estimated the rally in the city 3,800 miles east of Moscow drew 15,000 to 50,000 people.
Hundreds have rallied in the city centre every day this week against the arrest of Sergei Furgal, reflecting widespread anger over the arrest of the popular governor and a simmering discontent with the Kremlin’s policies.
Mr Furgal, the Khabarovsk region governor, was arrested on July 9 and flown to Moscow where he was put in jail for two months.
Russia’s Investigative Committee says he is suspected of involvement in several murders of businessmen in 2004 and 2005.
Mr Furgal has denied the charges, which relate to his time as a businessman with interests ranging from imports of consumer goods to timber and metals.
Khabarovsk residents dismissed the charges against him as unsubstantiated and denounced the Kremlin for targeting a governor they elected.
“It’s not only about this (whether Furgal arrest is legal or not). People are fed up with the way we are treated, that they (authorities) can simply take away our choice,” Mikhail Yerashchenko, one of the protesters, said on Saturday.
A member of the nationalist Liberal Democratic Party, Mr Furgal was elected governor in 2018, defeating the Kremlin-backed incumbent.
His victory was unexpected as he did not actively campaign and toed the Kremlin’s line, publicly supporting his rival.
People voted for him nonetheless, delivering a humiliating blow to the main Kremlin party, United Russia, that has been losing seats in regional administrations over the past two years.
During his two years in office, Furgal earned a reputation of “the people’s governor”.
He cut his own salary, ordered the sale of an expensive yacht the previous administration bought, met protesters when rallies took place and significantly reduced flight fares for residents in remote areas.
Last Saturday, crowds of reportedly up to 35,000 people rallied in the city centre. Protesters demanded that his trial be moved to Khabarovsk, with one of them saying “we have elected him, and it’s up to us to judge him”.
The protests, unauthorised by authorities, are the largest ever to have taken place in Khabarovsk, a city of 590,000.
Kremlin spokesman Dmitry Peskov called the situation “not standard” this week. Moscow has not yet appointed an acting governor 11 days after Mr Furgal’s arrest.
