Putin enacted a controversial law that designates NGOs as "foreign agents" if they receive funding from a foreign government. Moscow offices of Human Rights Watch and Amnesty International were raided this year.
Director of Russian advocacy group For Human Rights Lev Ponomaryov said the NGO community in Russia may cease to exist. Lyudmila Alexeyeva, from the Helsinki Group in Moscow, said a decision was made to get rid organizations "that irritate our leadership," state news agency RIA Novosti reports.
Putin defended the measure as part of an anti-corruption and transparency campaign. Human Rights Watch said more than 250 organizations like it were raided in Russia in recent months.
"Officials have harassed, intimidated, and even imprisoned political activists," the organization said. "The new laws and government harassment are pushing civil society activists to the margins of the law."
Thousands of people protested in Moscow this week on the anniversary of Putin's inauguration for a third non-consecutive term in office.
Ponomaryov said Putin's administration was trying to get rid of its opponents.
"We're enemies in the eyes of the president," he was quoted as saying.