The move is aimed at checking misuse of foreign funding by the voluntary organisations.
The Home Ministry has also discontinued submission of hard copies of such returns by the NGOs and from now on will accept only details filed online.
"All persons who are either registered or have been granted prior permission to receive foreign contribution, are once again advised to file their annual return for the financial year 2014-15 onwards online and it is informed that hard copy, if received, will not be accepted and treated as 'not received'.
As per new rules, any person, who receives foreign funds, has to submit digitally-signed report electronically with scanned copies of income and expenditure statement, receipt and payment account and balance sheet for every financial year beginning on April 1, within nine months of the closure of financial year.
The Home Ministry said many persons have submitted hard copy of the returns pertaining to financial years 2014-15 and 2015-16 "which have not been accepted and treated as if not received".