Russian President Vladimir Putin last year passed a law that requires non-governmental organizations to register as foreign agents if they receive funding from abroad. Prosecutors from the Russian republic of Tartarstan ordered registration from human rights group Agora in the latest sweep.
Agora spokesman Dmitry Kolbasin described the order to state news agency RIA Novosti as outrageous.
"Providing legal assistance to people detained at protests cannot be considered political," he said. "The demands are unfounded and unlawful and we will appeal."
Rights groups Amnesty International and Human Rights Watch described the NGO measure as "alarming."
The Moscow offices of Human Rights Watch, Amnesty International and Transparency International were raided by Russian authorities last month.
Putin was elected to a third non-consecutive term as president last year, an election that was marked by widespread protests.
He defended his position last week, saying targeting NGOs working in the country was aimed at transparency.