Russian police and tax inspectors have raided the offices of the human rights group Memorial and other civil society groups which get foreign funding.
Memorial is famous for documenting human rights abuses in Russia.
The US embassy in Moscow has voiced concern and asked the Russian government for an explanation.
A new Russian law says foreign-funded non-governmental groups (NGOs) linked to politics must register as "foreign agents" - a term which suggests spying.
In the worst repressions of the Soviet period the label "foreign agents" was used to denounce dissidents - or simply political rivals of Joseph Stalin - and could lead to execution.
Memorial says inspectors returned to its Moscow offices on Friday, having already seized 600 documents including accounts on Thursday.
A statement on the Memorial website said the inspections were directly linked to the new law on NGOs and the targeted groups' compliance with it.
Memorial director Arseny Roginsky, quoted by the Russian news website Vesti, said it was "a complete check on everything concerned with our sources of funding".
He insisted that the NGO law "will not change our position at all". "We won't refuse foreign donations, nor will we register as a 'foreign agent'," he said.
Pressure on NGOs
Russian President Vladimir Putin has accused foreign-funded NGOs of meddling in politics on behalf of foreign powers.
Two investigative reporters from state-controlled NTV television also turned up at Memorial's offices uninvited on Thursday. Memorial complained to police, who escorted the journalists out.
Last October NTV broadcast a controversial documentary called Anatomy Of A Protest 2, which alleged that anti-Kremlin protest leaders in Russia were funded by a Georgian MP. The leaders denounced the allegations as a fabrication. NTV is owned by Russia's Gazprom gas monopoly and is seen as close to the Kremlin.
A member of the Russian presidential Human Rights Council, Pavel Chikov, said up to 2,000 organisations had been targeted with inspections and searches this month, in connection with the NGO law.
Speaking to the Associated Press news agency, he said "it goes full circle across the whole spectrum - they're trying to find as many violations as possible".
Memorial has a representative on the Human Rights Council - Sergei Krivenko. Four other groups searched by the police also have representatives on the council, the Russian news website Vedomosti reports.
The council has complained to Russian Prosecutor-General Yuri Chaika about increased checks carried out on NGOs in 13 regions.
Last September the United States Agency for International Development (USAID) announced it had been ordered by the Russian authorities to shut down its operations. USAID has worked in Russia for two decades, spending nearly $3bn (£1.8bn) on aid and democratic programmes.