The Union Home Ministry said it has cancelled registration of 11,319 organisations that had not applied for renewal of registration under the Foreign Contribution Regulations Act (FCRA) by the June 30 deadline this year.
"Their validity of registration is deemed expired from November 1, 2016," it said.
In the list are about 50 orphanages, hundreds of schools and institutions such as the Indian Statistical Institute and reputed NGOs that works for street children.
In 2015, the Home Ministry cancelled FCRA registration of 10,000 non-government organisations because they did not file their annual returns for three years in a row.
Many of these organisations were defunct or did not want the FCRA registration in any case.
The centre's decision brings down the number of not-for-profit organisations permitted to receive foreign funding to 20,500, less than half of what it was two years ago when 42,500 were registered under the FCRA 2010.
The Foreign Contribution Regulation Act 2010- which replaced a 1976 law by the same name - ended the system of permanent registration, and required NGOs to seek renewal of their licence every five years.
The validity of FCRA registration of the NGOs was extended till October 31, 2016 but they were required to submit applications for renewal of registration by June 30.
The Home Ministry also said it had closed the application for FCRA licence renewal in 1,736 cases due to "non-submission of documents or deficient documents or other statutory shortcoming within the stipulated time".
These 1,736 NGOs include some branches of the Ramakrishna Mission, Mata Amritanandamayi Math as well as the Krishnamurthi Foundation of India, and they had applied online for renewal of their registrations before June 30, 2016.
The Ministry has now asked these 1,736 NGOs to submit their representations in support of deficiency in the application, through designated email email@example.com by November 8 failing which no representation will be accepted.
In its original form, the FCRA was enacted apparently to restrict flow of foreign funds to civil society groups during the 1975-77 Emergency.
Parliament had passed a stringent version of the FCRA in 2010, with the Congress-led UPA government insisting that NGOs that rely on foreign funds had to be prepared for greater scrutiny.
The Modi government has so far cancelled registration of more than 22,000 NGO for various alleged lapses.