While many expressed support for the arrested politician, some of the protest signs and chants were distinctly anti-Putin.
On Saturday, tens of thousands, including young people, the elderly and women with children in pushchairs marched through Khabarovsk's hilly streets in temperatures of over 30C, an AFP correspondent said.
Smaller rallies also took place in nearby cities and towns including Komsomolsk-on-Amur and Amursk and the Pacific port of Vladivostok in next-door Primorsky Krai region.
In rallies that lasted several hours, the crowds also massed outside the building housing the regional administration, chanting "Freedom!"
Protesters carried placards reading "Freedom for Furgal!" and cried out "As long as we are united we are invincible", as passing cars honked horns in support.
'We need him'
Demonstrators praised the arrested governor, saying he has done a lot for the region over the past two years.
"I am defending him because I am fond of him," said Anatoly Svechin, a 49-year-old Cossack, a member of the paramilitary group traditionally loyal to the Kremlin.
Another protester, Gennady Vasin, called the governor's detention an example of "political arbitrariness."
"We don't want Sergei Ivanovich to be taken away," said Gennady Yakovlev, using Mr Furgal's first name and patronymic. "We need him, we elected him."
Mr Furgal, a member of the nationalist LDPR party, was elected with a large majority in 2018, trouncing a candidate of the ruling party backed by Putin.
Many of the protesters say the charges are politically motivated and question why investigators waited so long to accuse a public official who should have undergone background checks.
Investigators say Mr Furgal organised the murders of several businessmen in the Far East in 2004 and 2005.
The protesters called for a "fair trial" for the governor, and not in Moscow, where he is being held since his arrest.
"It's our governor! And we will defend him!", they shouted.
As with previous protests, the rally was not approved by the authorities, but police made no moves to disperse it.
'Putin's endless lies'
Russia's main opposition leader Alexei Navalny cheered the protests.
"An entire city - Khabarovsk - refused to believe Putin's endless lies about the 'justice' of his courts and the 'honesty' of his elections," Mr Navalny said on Instagram.
Protesters took to the streets even after authorities warned of the dangers of the coronavirus epidemic and after the FSB security service said on Friday it managed to "prevent a terror attack" in Khabarovsk.
Last Saturday, tens of thousands also poured onto the streets of Khabarovsk and nearby towns, and hundreds protested throughout the week.
The rallies come as popular discontent is growing across the country over the authorities' handling of the coronavirus crisis and falling real incomes.