The home ministry in a circular said a large number of NGOs, which were registered under the Foreign Contribution (Regulation) Act, are yet to submit their annual returns for five years -- 2010-11 to 2014-15 despite giving a final opportunity to do so.
"It may be noted that the failure to upload annual returns by NGOs may lead to cancellation of registration/ renewal granted to them," Joint Secretary (foreigners' division) in the home ministry Mukesh Mittal said.
Earlier, the ministry had said starting May 15 and till June 14, all such NGOs can upload their missing annual returns along with the requisite documents within 30 days.
No compounding fee will be imposed on them for late filing of annual returns during this period and this exemption was a one-time measure, it said.
As per the rules, the renewal of registration under FCRA cannot be granted unless the annual returns are uploaded to the FCRA website by the organisation.
The government is estimated to have cancelled the licences of nearly 7,500 NGOs in last three years after they failed to disclose their income and expenditure statements.
The government scheme is not applicable to NGOs like Greenpeace, Sabrang Trust, Islamic Research Foundation and 1,300 others whose registrations have been cancelled for allegedly violating various provisions of the FCRA.
In November, 2016, the government had directed more than 11,000 NGOs to file applications for renewal of registration by February 28, 2017.
However, only 3,500 NGOs filed applications for renewal while the registration of more than 7,000 NGOs were deemed expired due to non-filing.