Thousands of people across Russia took to the streets yesterday demanding the resignation of Vladimir Putin, in the largest show of discontent since he came to power more than a decade ago.

Opposition movements called the nationwide "Day of Wrath" to express growing discontent at falling living standards following years of oil-fuelled growth. The protests followed weeks of sustained demonstrations across Russia that have riled a leadership that does not forgive displays of unrest.

Cries of "Freedom" and "Putin resign" filled the main square in Kaliningrad, where up to 5,000 people gathered in pouring rain. The Baltic territory, which is nestled between Poland and Lithuania and separated from the Russian mainland, has been the site of some of the largest protests to date.

"We want the government to start treating us like people, not like slaves," said Kirill, a 22-year-old student. Protesters called for free elections and complained about widespread corruption, high unemployment and rising prices.

Russia's first major anti-Putin demonstration was held in Kaliningrad on 30 January, drawing 12,000 people and shocking local leaders and the Kremlin. "It really surprised us," said Konstantin Polyakov, deputy head of the regional parliament, or Duma, and member of the ruling United Russia party. "We didn't think so many people would turn out, to be honest." The Kremlin was obviously shaken, dispatching a high-level delegation to the Baltic exclave and firing its Kaliningrad adviser, Oleg Matveichev.

Saturday's protest had been banned, and opposition leaders withdrew calls for an organised demonstration, fearing violence. Yet several thousand showed up anyway, organising through the internet and word of mouth.

"The general public in the regions is beginning to recognise that it is Putin who is actually to blame for various troubles they have – increased cost of living, communal tariffs, taxes and no growth in real wages," said Vladimir Milov, a co-leader of Solidarity, an umbrella opposition movement.

Regional and local elections held on 14 March appear to support that theory. United Russia, the party created with the sole purpose of supporting Putin's rule – he is currently prime minister – garnered unprecedentedly low results, losing its majority in four of eight regions and giving up the mayorship of Irkutsk, Siberia's largest city, to a Communist candidate who took 62% of the vote.

In Kaliningrad, protesters wore badges criticising United Russia and held aloft mandarins, the fruit that has come to symbolise the region's unpopular governor, Georgy Boos, a Muscovite appointed by Putin.

Few, even those in opposition, believe the Putin government will fall. "It will take time," Milov said. "But just two years ago it would have been impossible to imagine mass demonstrations making political demands like the resignation of Putin's government."

A poll this month by Russia's Public Opinion Foundation found that 29% of Russians were ready to take part in protests, up from 21% in February.

More than 1,000 people turned out on Saturday in the port of Vladivostok, where discontent has steadily grown since the government imposed a tax on imported cars. About 500 people rallied in Irkutsk and St Petersburg. Riot police broke up an unsanctioned rally in Moscow violently and arrested 50 activists. Authorities also shut down a website set up for the "Day of Wrath", www.20marta.ru, and in the northern city of Arkhangelsk an opposition leader was arrested and charged with theft.

In Kaliningrad, on the border with the European Union and far from the seat of power, the police presence was minimal, although agents in plain clothes roamed through the crowd.

"Our population is different from Russia," said Polyakov, sitting in his office adorned with photos of Putin and President Dmitry Medvedev, in what is, technically, Russia. "Our people, especially the youth, travel more to Europe than to Russia. There's no reason to go there."

In an implicit criticism of Moscow politics, he added: "We're more European – more relaxed, less eastern. And we're more democratic." Despite the protesters' rhetoric, Polyakov argued that Putin's popularity in the region remains high. His wife, Lyudmila, was born here and visits regularly.

But local authorities, acting in concert with Moscow, reacted with unusual harshness to Kaliningrad's wave of protests. They banned a rally in the city centre, saying protesters could gather in a stadium on the outskirts instead.

In an ironic twist, the government has been forced to give in to opponents of liberal market reforms. Following the Kaliningrad protest, it has promised to slow the post-Soviet desubsidisation of utilities like heat and water. That will only widen a budget deficit expected to exceed 6% of GDP this year.

"The leadership is scared," said Solomon Ginzburg, an independent deputy in the regional Duma. "I have been saying the Kaliningrad region is an indicator – in nine months, it will be all over Russia."