Germany and France summoned Russian diplomats in Berlin and Paris on Wednesday, after Russia launched a series of raids on international non-governmental organisations (NGOs) across the country amid a wider crackdown on critics of the Kremlin.

The sweeps, billed as an attempt to weed out "foreign agents", targeted human rights organisations, environmental advocates, women's groups, non-Orthodox churches, charities and at least one French language school. Among the sites raided were the Moscow offices of the rights groups Amnesty International, Human Rights Watch and Transparency International.

"This is the planned destruction of the NGO sector in Russia," said Lev Ponomarev, head of For Human Rights, a Russian group that was targeted on Monday. "It's a war on NGOs and the strengthening of the authoritarian police state."

Catherine Ashton, the EU high representative, said she was "concerned" by the raids and said they formed part of "a trend that is deeply troubling".

"The inspections and searches launched against the Russian NGO community and conducted on vague legal grounds are worrisome since they seem to be aimed at further undermining civil society in the country," she said in a statement.

The German foreign ministry summoned the number two diplomat in the Russian embassy in Berlin on Tuesday "to express the German government's concern" over the raids. Two German NGOs in Moscow and Saint Petersburg were raided earlier this week. Hans-Gert Pöttering, chairman of the Konrad-Adenauer-Stiftung foundation in Saint Petersburg, said officials had seized four of the group's computers there.

The French foreign ministry sent a note to its Russian embassy on Wednesday demanding an explanation, but said in a statement that the ambassador had been "invited" for a discussion.

The US embassy in Moscow said via its Twitter feed: "It is with great concern that we are following reports of unprecedented inspections of NGOs across Russia."

Prosecutors, tax inspectors and officials from the justice ministry have conducted unannounced "checks" on more than 80 organisations around Russia, said Pavel Chikov, the head of Agora, a legal group that provides assistance to civic and political activists. Thousands more are expected to be targeted, he said. Agora was raided on Wednesday.

The sweep comes eight months after Vladimir Putin, the president, signed a widely criticised law demanding that NGOs which receive funding from abroad label themselves as "foreign agents". Critics said the law was reminiscent of Soviet-era efforts to demonise foreigners and those "collaborating" with them.

A handful of groups, including For Human Rights, have refused to follow the law on principle. "I am not a foreign agent," said Ponomarev, arguing that following the law – which includes stamping "foreign agent" on all paper and electronic documents – would make his work impossible.

There was little noise about the law since its signing until last month, when Putin used a Valentine's Day meeting with officers from the Federal Security Service (FSB) to remind them of its existence. "No one has the right to speak for all of Russian society, especially those who are directed and financed from abroad and thus serve the interests of others," Putin said. "Today we have set the order of NGO activity in Russia, including funding from abroad. These laws must, without a doubt, be fulfilled."

Within weeks, inspectors were fanning out across the nation.

On Wednesday, they arrived at the central Moscow office of Human Rights Watch, a New-York-based group that has operated in Russia since the fall of the Soviet Union.

"This is the first time in over 21 years that we have been inspected," said Rachel Denber, deputy director of HRW's Europe and Central Asia division. "The scale of these inspections has been massive and unprecedented and is part of a much broader campaign to limit civil society." It was also, she said, "part of a broader effort to brand those organisations that are connected to foreigners as enemies, as suspect".

Putin returned to the presidency last year amid unprecedented protests. While street action against him has died down, anger with the powerful longtime leader – particularly among the urban middle class – remains strong.

The crackdown against critics has been relentless. More than 20 people are facing jail for participating in a protest on 6 May and criminal charges have been brought against a host of opposition leaders. A series of laws has been introduced to clamp down on dissent.

The Kremlin has also promoted a growing suspicion of foreigners, particularly Americans. Last year, Russia shut the office of the US Agency for International Development after accusing it of trying to influence Russia's elections. Americans were banned from adopting Russian children late last year.

"Russia's leadership has made very clear for at least a year, and Putin himself has not missed an opportunity to say, that when foreigners raise human rights issues in Russia, he believes it to be an infringement on national sovereignty," said Denber.

The tax inspector and three officials from Russia's prosecutors office that visited HRW's office on Wednesday were accompanied by a camera crew from NTV, a state-run television channel owned by the gas giant Gazprom that has aired regular propaganda films accusing Russian human rights workers and opposition activists of acting on orders from Washington. NTV ran similar footage of a raid on Ponomarev's group earlier this week.