The European court of human rights has ruled that Russia violated the rights of the opposition leader Alexei Navalny by placing him under house arrest in 2014 during an embezzlement investigation that his supporters described as politically motivated.

The ruling comes amid speculation that Russia is considering leaving the Council of Europe, which oversees the European court of human rights, or may see its membership suspended in the coming months.

The Council of Europe and the ECHR are separate institutions from the European Union.

The court in Strasbourg said in a judgment the house arrest order had not been justified and it was “apparent he had been treated in that way in order to curtail his public activities”.

Navalny wrote “victory” on social media in response to the ruling. “I am sure this ruling will have important consequences for all those in Russia who are constantly subjected to this kind of lawlessness.”

But that could change if Russia breaks with the European court of human rights in June, leaving thousands of Russians who appeal each year to the European body without legal recourse for violations of their rights.

Human rights activists have worried that Russia’s potential exit, referred to as “Ruxit”, could have a knock-on effect for Russia’s vast system of law enforcement and prisons.

“It’s very important for the whole law enforcement system,” said Natalia Taubina, a veteran human rights activist and director of the Public Verdict Foundation. “The judgments really can make a difference. It would be a huge loss for us and for Russians not to be able to use this system any more.”

New polling showed that Russians broadly support the option to seek protection for their rights from the European court of human rights. The independent Levada Center reported that 66% thought it was “important” for Russians to be able to petition the court, while 88% gave a similar answer to an online survey run by the Ivan Nizgoraev Methodology Lab and the Public Verdict Foundation.

But many, especially older Russians and those living outside of major cities, told the Levada Center they knew little about the court’s activities.

The conflict has been brewing since Russia’s annexation of Crimea in 2014, which led to a suspension of Russia’s voting rights in the parliamentary assembly of the Council of Europe. Russia responded by boycotting the assembly and suspending its annual £28m payments to the council.

In June, after two years of non-payments, Russia can be suspended from the council or quit in protest. Russia has threatened to exit the council if it cannot participate in the elections for the body’s next secretary general.

“The question of Russia’s participation in the election of the CoE secretary general is a critical moment for Russia’s membership in this organisation,” a foreign ministry official said late last month.

Russians submit among the largest number of petitions to the organisation out of any of the Council of Europe’s members, and the country has been ordered to pay out millions of euros in compensation each year.

In 2018, the court said it had more than 11,700 cases pending against Russia for violations of the right to life, crackdowns on free expression, holding detainees in inhumane conditions, and other violations under the European convention on human rights. Moscow has complained about the court’s bias but has generally abided by its rulings, which it is required to as a signatory to the convention.

Prominent rulings have included the 2012 conviction of the punk protest band Pussy Riot, the investigation into the 2006 murder of the journalist Anna Politkovskaya, a suit brought by shareholders in the defunct oil giant Yukos and others.

Ahead of the potential break, the court has issued a number of high-profile decisions, including a January ruling that Russia must pay Georgia €10m for the mass deportation of Georgian citizens from Russia in 2006.

Thorbjørn Jagland, the council’s secretary general, has warned the break could have grave consequences and its effects could be compounded by the UK’s exit from the EU.

“The Council of Europe is the only place where Russia is connected to Europe in a binding judicial way,” Jagland told the Financial Times earlier this week. “We will see a different Russia. We will have a new dividing line in Europe.”

The council’s spring session began on Monday with speculation that it could be Russia’s last as a member of the body.

“Time is running out and negotiations between the CoE and Russian officials, despite significant efforts being done on the CoE side, seem to be stuck, which means that the likelihood of ‘Ruxit’ is increasing day by day,” wrote Konstantin Baranov of the International Youth Human Rights Movement. “The Russian side has raised the stakes as high as possible, and it would be very difficult for them (if ever possible) to retract in June or after it.”