The home ministry has cancelled the registration of these NGOs, saying they have failed to comply with rules.
A home ministry letter says that 10,343 associations had not submitted annuals returns since 2009-12. Notices were sent to them to file returns by October last year, but only 229 associations responded.
The registration of the remaining 8,975 organisations has been cancelled.
The Foreign Contributions Regulations Act requires organisations receiving foreign funds to give details of the contributions received, their source and the purpose for which they were used, every year.
NGOs and lobby groups have been on the government’s radar since last year after a report by the Intelligence Bureau said they had been stalling economic growth by campaigning against power projects, mining and genetically modified food.
Last week, the home ministry placed the Ford Foundation on its watch list, saying it wanted to ensure that its funds were utilised for “bonafide welfare activities without compromising on concerns of national interest and security”.
Earlier, Greenpeace India was barred from receiving foreign funds. The government alleges that it has “prejudicially affected the economic interest of the state”.