The move followed a raid two days earlier on the headquarters of Amnesty International, Radio Free Europe/Radio Liberty reported.
Russian officials said they were checking to make sure nongovernmental agencies are complying with Russia's new laws on foreign financing. Rachel Denber of Human Rights Watch said the Russians told them they were conducting an "unannounced audit" of their Moscow office.
The head of Amnesty International in Russia said the raiders demanded documents that were already on file with the government.
Russia has been clamping down on international nonprofits operating in the country, forcing some to register as foreign agents.
The Russian parliament has passed strict new rules governing how international aid groups can operate in the country.