Russian authorities searched the Moscow offices of Human Rights Watch and three other prominent advocacy groups on Wednesday, part of a wave of hundreds of inspections that activists say is a campaign to silence criticism of President Vladimir Putin.

Since returning to the Kremlin in May, Putin has tightened controls on non-governmental organizations, requiring those with foreign funding to register as "foreign agents" – a term echoing, for some, Stalin-era political repressions and Cold War spying.

The Kremlin says it is working to prevent foreign governments meddling in Russian politics, but activists see the visits by prosecutors and other authorities ranging from tax officials to fire inspectors as harassment.

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"This is part of a massive, unprecedented in its scale wave of inspections of NGOs throughout Russia... covering hundreds and hundreds of groups," said Rachel Denber, Deputy Director of the Europe and Central Asia Division of Human Rights Watch.

"Most immediately it is an effort to intimidate. More broadly it's part of an effort to discredit ideas about human rights and civil society, to somehow tar them as foreign and suspect," she said by telephone from New York, where Human Rights Watch is based.

The United States has said it is very concerned about the inspections and European Union Foreign Policy chief Catherine Ashton on Tuesday described what she called the "raids" on NGOs as part of a trend that was deeply troubling.

Germany complained to Russia on Tuesday about the inspections, including visits to two German think-tanks, saying the action could harm bilateral ties already strained by the Cyprus crisis.

Federal migration officials visited the offices on Wednesday of a rights group run by Svetlana Gannushkina, one of Russia's most prominent campaigners to help refugees and migrants, Gannushkina said.

"I am a member of the state commission for migration politics. We are not working against our government - I'm afraid that our government is working against our people," Gannushkina told Reuters.

Gannushkina said tax and migration service officers showed up unannounced and demanded passports of employees and visitors who did not look Russian.

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"This is undoubtedly done to apply pressure, it's undoubtedly done to put pressure on civil society."

Denber said a tax officer and three prosecutorial officials were polite but spent hours in the Human Rights Watch office in an unannounced inspection, demanding copies of registration papers and a slew of other documents. They were unarmed.

Authorities on Wednesday also visited offices of anti-corruption group Transparency International Russia and Agora, a human rights organization.

On Monday, the Moscow offices Amnesty International were searched in checks the human rights advocacy group said showed "the menacing atmosphere for civil society" in Russia.

The Kremlin denies cracking down on critics, but Putin's own advisory council on human rights has asked Prosecutor General Yuri Chaika to explain the wave of searches.

Pavel Chikhov, the head of Agora, said the searches are aimed at gathering evidence of activities that would oblige them to register as "foreign agents" under the law.

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Russia's leading rights organisations, including the country's oldest rights group Memorial, election-monitoring body Golos and the Moscow Helsinki Group, have refused to register in defiance of the law.

The penalties for failing to comply include six months' suspension without a court order and, for individuals, up to three years in jail.

Putin, facing the biggest protests of his 13-year rule last year, accused foreign governments, including the United States, of meddling in Russia's domestic politics, and pro-Kremlin media said anti-Putin demonstrators were payed by foreigners to take to the streets.

Last autumn, Moscow expelled the U.S. Agency for International Development (USAID), saying it had tried to influence elections.