But the warning has not impressed or deterred a younger generation of protesters who are fed up with rampant nepotism, exasperated by the lack of accountability, and stifled by the lack of opportunities on offer in Russia today.
Their grievances are directed less at Putin himself than at a system that has institutionalized graft and accelerated inequality. In some ways they are reminiscent of the frustration of younger, educated Arabs in Cairo and Tunis in 2011, but it is unclear if Russia's anti-corruption movement can effect real change.
In Moscow, where the largest of dozens of protests took place, at least 500 people were detained -- carried and frog-marched into police vehicles. The authorities had warned that the rally, called by opposition leader Alexey Navalny, was against the law.
A young geologist called Sergey Pravov was among those arrested. "We started singing the national anthem," he told CNN. He added with a smile: "We just got to the 'free country' part, when we were taken by the police and thrown into the bus."
He told CNN that young people had taken part because they "are tired of the impunity of officials and their children and relatives who can get away with anything. "
"They are tired of living below the poverty line while people they pay to rule wisely are swimming in gold," Pravov says.
Pravov was eventually released, but Maksim Malysh was not as lucky.
Malysh was charged with resisting a police officer and given ten days in jail. The 22-year-old says he was meeting a friend at a café, went outside to film the protest, and was immediately pushed to the ground.
"I didn't resist but they still beat me up," he says. "They told me to relax my body. I did it and got hit on the head, dragged into the bus."
A photograph of Olga Lozina being carried away by police officers went viral. She told CNN she had just left a McDonald's on Pushkinskaya Square and wasn't even participating in the protest.
When her mother protested the arrest of a young man, she was detained, as was Olga's sister. When Olga intervened, she too was arrested.
"I was in shock," Lozina told CNN. "I took a few steps towards them and that was the moment when policeman grabbed me by the hand."
She said she was arrested and bundled into a bus with more than 30 others, and wasn't released from the police station until 6 am the following day. She has a court appearance next month for attending an illegal protest.
Even though Lozina, a graduate of the Physical-Technical Institute in Moscow, had no plans to get involved in the rally, she said she agreed with Navalny, who for years has been a thorn in the side of the Kremlin.
"We all know that Russia is corrupted," she said. "And Alexey Navalny just showed the schemes, the process, made it public, opened it to the public eye."
Corruption front and center
Navalny has made corruption the big issue in his campaign against the government, and has focused on Prime Minister Dmitri Medvedev.
An investigation by his Anti-Corruption Foundation, promoted in a slick 49-minute video posted online, claims Medvedev has amassed a "corruption empire" of lavish properties, luxury yachts, and vineyards across Russia.
The video has been viewed more than 14 million times on YouTube alone.
Medvedev's spokeswoman, Natalya Timakova, told state-run news agency RIA Novosti: "It is pointless to comment on the propagandistic outbursts of a convicted opposition figure, who has already announced he is running some kind of election campaign and fighting against the authorities."
After being arrested on Sunday, Navalny said the protests had "shown there are quite a large number of voters in Russia who support a candidate that speaks against corruption."
Journalist Mikhail Zygar sees a tempting target in Medvedev for Russia's fledgling opposition.
"The majority of under-25s in Russia think we have a genius foreign policy but a terrible domestic one," Zygara wrote on Facebook. They support Putin's actions abroad, he says, but think Medvedev incapable of enacting necessary social reforms at home.
The Prime Minister has been criticized for seeming oblivious to hardship. When in Crimea last year meeting people who were complaining about inflation and hardship, Medvedev responded: "There is no money. But hang in there."
The Kremlin reacts
The government -- if not rattled by the latest demonstrations -- has certainly taken notice.
Kremlin spokesman Dmitri Peskov claimed, without offering any evidence, that protest organizers had offered young people financial incentives to take part and had put them "in a dangerous, life-threatening situation."
The Deputy Interior Minister, Igor Zubov, followed up with a darker warning, saying that "if there is an increase in provocative actions in the future, the available arsenal which we can use is much wider."
But some Russian politicians have taken a more conciliatory line. On Wednesday Valentina Matviyenko, chairwoman of Russia's upper house of parliament, said government representatives
"must meet with people and understand why they protest."
"Authorities should not simply [pretend] that nothing is happening," she said.
Digital alternatives to state media
Navalny has recognized that despite the immense reach of state media and the stifling of independent networks, the internet and social media offer an avenue to potential supporters. Websites such as Meduza, whose tagline is "The Real Russia. Today," have found an audience eager for their alternative take on events.
Opinion polls also suggest persistent anger with corruption. In the latest survey carried out by the Levada Center
, 65% described corruption as absolutely unacceptable. Few Russians blame Putin: only 17% think corruption has worsened since he became President. But many say it's endemic: 45% believe Putin wouldn't succeed in fighting corruption, the highest percentage recorded in five years.
Sergey Pravov, the young geologist, hopes he hasn't put his career at risk by taking part in Sunday's protest and getting arrested in the process. He insists he's not demanding nor expecting an "immediate power-shift."
But he also says that Russia is far different from the Soviet Union and sees the possibility of change in decades to come.
Younger Russians, he says, "want to be in the future, they want to live in a different country."