Russian authorities detained more than 1,000 protesters in Moscow on Saturday, in an attempt to quash a recent surge in protest mood that has spooked the Kremlin. Police also arrived at the homes of multiple opposition figures with search and arrest warrants, and called the editor-in-chief of the country’s leading independent television station in for questioning.

Opposition politicians called Saturday’s protest in response to a decision not to allow a number of independent candidates to stand in a September election to Moscow’s municipal parliament. Last weekend, the Russian capital saw the largest anti-government demonstration for years over the issue.

Taken by surprise, authorities responded over the past week by launching a series of legal procedures against various opposition figures, alternating between the sinister and the absurd. Alexei Navalny, the highest profile opposition politician, was arrested outside his house earlier in the week as he stepped out to go jogging and buy his wife flowers for her birthday; he has been sentenced to 30 days in jail. Others received midnight knocks on the door from investigators, who demanded to search their properties and branded them suspects in the crime of “hindering the work of the electoral commission”.

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Sources told Russian media outlets that a department of the FSB security services, the successor of the KGB, is running the cases against opposition leaders. The FSB apparently believes there is a foreign hand behind the protests, seeking to destabilise Russia.

To stop crowds gathering outside the Moscow mayor’s offices on Saturday, police cordoned off whole sections of Tverskaya, one of Moscow’s main thoroughfares. Large groups of protesters tried to find a way to the mayoralty, winding through courtyards and side streets, and more often than not encountering police cordons. Police put the number of protesters at 3,500, but the real figure was likely much higher.

As of early evening, more than 630 people had been detained by police according to independent observers, a few of them violently. It was not immediately clear what charges, if any, police would bring against them.

From a loudspeaker, police shouted at the crowds that they were taking part in an unsanctioned demonstration, that they faced being held responsible for breaking the law, and that they were “blocking the way for fellow citizens”. Undeterred, groups of protesters chanted the same back at police.

“This is the end of Russia’s 30-year experiment with elections,” said Grigory Yavlinsky, a veteran Russian liberal politician, as he tried unsuccessfully to cross a police barrier and make his way to Tverskaya. Yavlinsky, who came third in the 2000 presidential election in which Putin first won the presidency, said that “with each year the elections are less and less real, but this is really the end”. He said it was unclear what the future of the protest movement holds.

In Russia, decisions about which candidates are allowed to take part in elections are often taken in the corridors of the presidential administration rather than by the electoral bodies. When a series of independent opposition candidates managed to clear the hurdles required to register for the Moscow city elections, collecting several thousand signatures from voters, the electoral commission simply claimed that many of the signatures were fake and it would not register the candidates in any case. This prompted the wave of protests, turning fairly meaningless local elections into a major political talking point.

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Lyubov Sobol, a Navalny associate who wants to stand in one Moscow district, is currently on hunger strike and staged a sit-in at the Moscow electoral commission earlier this week. At one point she was carried out by guards, together with the sofa on which she was sitting, and she was arrested on her way to the protest on Saturday.

Police also raided a studio where Navalny associates were running a protest livestream, and arrived at TV Rain, Russia’s leading independent television station, which was also streaming the protests. The editor-in-chief was called in for questioning, the channel said.

The surprise wave of summer protests is the biggest since 2012, when months of discontent culminated in a rally on Moscow’s Bolotnaya Square the day before Vladimir Putin was inaugurated for a new term as president. After that rally, which saw violent clashes between police and protesters, a crackdown was launched, with a number of protesters handed lengthy prison sentences.

Now, authorities will again have to decide whether to step back or crack down, at a time when Putin’s ratings are slipping and his ruling United Russia party is widely despised. In recent months, the Kremlin has backed down when faced with public protests, mainly over local issues such as the construction of a new cathedral in a public square in the city of Yekaterinburg.

Putin has not yet commented on the protests. The Russian president, undeterred by any potential symbolic resonance, climbed into a miniature submarine as the police made arrests on Saturday and descended to the seabed in the Gulf of Finland to inspect the ruins of a second world war submarine.