MOSCOW – A court on Wednesday ruled the political movement of Aleksei A. Navalny as extremist, a notable broadside from President Vladimir V. Putin, who also sent a message to President Biden ahead of their meeting next week: Russian internal affairs are not up Discussion.

The judicial decision – almost certainly with the blessing of the Kremlin – seemed to push the resistance against Putin further underground after years of efforts by the Russian government to suppress dissenting opinions entered a new, more aggressive phase for several months. Under the law, Mr Navalny’s organizers, donors or even social media supporters could now face criminal prosecution and face jail terms.

The ruling increases the commitment of the Geneva summit to Mr Biden, who has promised to defend himself against Mr Putin’s violation of international norms. But the Russian President has said that while he is ready to discuss cyberspace and geopolitics with Mr Biden, he will not have talks about how he governs his country. The question is how much Mr Biden accepts these demands.

“The views on our political system can be different,” Putin told the heads of international news agencies last week. “Please give us the right to organize this part of our life.”

The June 16 Geneva meeting will come after months in which Mr Putin has dismantled much of what remains of Russian political pluralism – and made it clear that he would ignore Western criticism.

Mr Navalny was arrested in January after returning to Moscow after recovering from poisoning carried out by Russian agents last year, according to Western officials. Since then, thousands of Russians have been arrested during protests; opposition leaders have been imprisoned or forced into exile; Online media were branded as “foreign agents”; and Twitter and other social networks have come under pressure from the government.

“The state has decided to fight all independent organizations with total bombing,” said Nawalny’s anti-corruption foundation – one of the groups declared extremist on Wednesday – in a Twitter post anticipating the verdict.

The Kremlin denies having played any role in the campaign against Navalny and his movement and insists that Russia’s judiciary is independent. However, analysts and lawyers largely see the courts as subordinate to the Kremlin and the security services, especially in politically sensitive cases.

Mr Putin has already signaled that he will reject any criticism of the Kremlin’s handling of the Navalny case by claiming that the United States has no power to teach others. At Russia’s annual economic conference in St. Petersburg last week, Putin repeatedly referred to the January arrests of Capitol rioters in Washington when challenged over repression in Russia or its ally Belarus.

“Look at the sad events in the United States where people refused to accept the election results and stormed Congress,” Putin said. “Why are you only interested in our non-systemic opposition?”

The “non-systemic opposition” is the Russian term for factions that are not represented in parliament and that openly demand Putin’s impeachment. For years they were tolerated, even if they were closely monitored and often persecuted. The court’s ruling on Wednesday signaled that this era of tolerance is coming to an end.

Prosecutors harassed Navalny and other opposition activists, mostly on pretexts such as violating rules for public gatherings, laws unrelated to their political activities, or, more recently, anti-gathering regulations designed to limit the spread of the coronavirus.

Behind the scenes, according to Western governments and human rights groups, the Kremlin had gone further: murdering or expelling journalists, dissidents and leaders of the political opposition in exile. Mr Navalny only barely survived an attack with a chemical weapon last summer. In 2015, another opposition leader and former First Deputy Prime Minister of Russia, Boris Y. Nemtsov, was shot dead with a pistol. But officials denied any role in these actions.

The dissolution of Mr Navalny’s nationwide network marked a new phase in the fight against dissent through a formal, legal process to dissolve opposition organizations despite the country’s 1993 Constitution guaranteeing freedom of expression.

The Kremlin’s campaign against the opposition increased after Navalny returned from Germany in January, where he received medical treatment after the neurotoxin attack. Police arrested Mr. Navalny at the airport and a court sentenced him to two and a half years in prison for violating parole on conviction in a case of embezzlement alleged by a human rights organization to be politically motivated.

In power since 1999, either as Prime Minister or President, Mr Putin has gradually tightened the screws on dissent and opposition. In a long twilight of post-Soviet democracy during his rule, elections took place, the internet remained largely free, and opposition was tolerated to a limited extent. His system has been called “gentle authoritarianism”.

But prosecutors this spring demanded that the court outlaw Mr Navalny’s move by using a term that compares its members to terrorists without bothering to publicly argue that the nonprofits were, in fact, seditious organizations . The evidence was classified and the case was held behind closed doors in a Moscow courtroom.

A lawyer representing the organizations, Ivan Pavlov, who had access to the evidence but was not empowered to disclose it, said after a preliminary hearing that it was not convincing and that he would publish as much as the law allows . Within a few days, police arrested Mr. Pavlov on charges of divulging secret evidence in another unrelated case, in what looked like a warning to avoid an aggressive defense of Mr. Navalny’s organization. He faces up to three years in prison.

According to Russian legal experts, the anti-extremism law offers a lot of scope for comprehensive action against the opposition in the coming days or months, but it remains unclear how it will be enforced.

According to the law, the organizers of the group face prison sentences of up to 10 years for continuing their activities. Anyone who donates money can be punished with up to eight years in prison. Public comments such as social media posts in favor of Mr Navalny’s groups could also be prosecuted in support of extremists.

The case was directed against three non-profit groups, Navalny headquarters, the Anti-Corruption Fund and the Civil Rights Defense Fund. In a preliminary ruling last month, the court ordered the activities of some of these groups to be suspended.

Pending the final verdict, Mr. Navalny’s staff disbanded one of the groups, Navalny’s headquarters, which operated its network of 40 political offices, before the court had a chance to designate it as an extremist group. Mr Navalny’s staff said they hoped some offices would continue to operate as independent, local political organizations.

“Unfortunately, we have to be honest: it is impossible to work in these conditions,” said an adviser to Mr Navalny, Leonid Volkov, in a YouTube video, warning that continuing the operation would prosecute supporters of the opposition leader. “We are officially dissolving the network of Navalny offices.”

When they announced the case in April, prosecutors argued that Mr Navalny’s groups were in fact riotous organizations disguised as a political movement. In a press release, the prosecutor said that “under the guise of liberal slogans, these organizations are busy creating conditions for the destabilization of the social and socio-political situation”.

Since he is forbidden from founding a political party, Mr Navalny has worked for various non-governmental organizations instead. Despite relentless pressure from the Russian authorities, these groups have for years insisted on promoting an anti-corruption campaign that frustrated and embarrassed Mr Putin, and have often used social media to great effect.

Mr Navalny’s movement was the most prominent in Russia, openly calling for Mr Putin’s ousting through elections, and its supporters say the Kremlin is determined to crush those efforts before they can bear fruit.