However the Russian government has defended the move saying it is necessary for national security.
A total of 376 deputies in the State Duma voted for the amended bill, while 10 in the chamber, which is heavily dominated by supporters of President Vladimir Putin, voted against.
The proposed law, which must still be passed in a third reading before going to the upper house, seeks to prevent NGOs from doubling as fronts for subversive foreign political causes, for foreign intelligence agencies, and for money laundering, the government says.
Critics in Russia and abroad fear the law will be used to clamp down on the country’s buoyant NGOs, one of the last independent sectors in Russia, where the media, parliament and big business are seen as increasingly under Kremlin control.
The 74 pages of amendments sought to water down an earlier version that was passed on November 23, provoking a storm of protest from NGOs, the United States and the European Parliament.
Supporters say the proposed measures are similar to laws in the US and other Western countries designed to monitor the flow and use of funds sent from abroad to groups registered as charities, human rights organisations and pro-democracy advocates.
“It’s clear that this law was indispensable,” Sergei Popov, from the pro-Putin United Russia party, said. “The goal is to have financial controls. Any civilised state would do the same thing.”
Opponents accuse the Kremlin of trying to neuter one of the country’s last independent sectors in order to prevent the development of a pro-Western, pro-democracy movement as in Ukraine and Georgia, where popular revolutions in the last two years ousted entrenched leaders after rigged elections.