The list includes top universities like Delhi University and Jawaharlal Nehru University, the Supreme Court Bar Association and Escorts Heart institute.
Cancellation of license amounts to putting a stop to the foreign funds being received by these organisations.
The decision to cancel the registration of these entities under the Foreign Contribution Regulation Act (FCRA) was taken by the Home Ministry after examining their activities. A number of anomalies were allegedly found. Non-filing of annual returns was one of them.
Other prominent organisations whose licences were cancelled include Punjab University, Gujarat National Law University, Gargi College, Lady Irwin College, Vikram Sarabhai Foundation and Kabir floated by Deputy Chief Minister of Delhi, Manish Sisodia.
All associations were given a notice by the Foreigners Division of the Home Ministry with adequate time to reply before their FCRA licences were cancelled, official sources said.
The last round of crackdown happened in April this year. Licences of almost 9,000 NGOs were cancelled in April for allegedly violating FCRA rules.
(With inputs from PTI)