Without the licences the NGOs will not be able to receive overseas donations, which could likely impair their day-to-day operations.
That leaves only 13,000 NGOs with licences in India where charities, especially foreign-backed ones like Greenpeace, have come under increased scrutiny since Prime Minister Narendra Modi came to power in 2014.
India reduces citizenship fee for Hindus, other minorities from Pakistan
A major crackdown began in early 2015 after an intelligence report said that groups like Greenpeace were damaging the country's economy by campaigning against key development projects.
The government has cancelled licences of thousands of NGOs since then, citing misuse of overseas donations to harm the country's growth.
Critics have argued that the apparent clampdown was an attempt to stifle voices of dissent.
An Indian charity running schools for low-caste Dalit children said last week it was set to close down after its foreign funds were blocked over alleged threats to national unity.
The home ministry said the charity had engaged in "undesirable activities aimed to affect prejudicially harmony between religious, racial, social, linguistic, regional groups, castes or communities".
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