Rijiju said thousands of NGOs, which were registered under the Foreign Contribution Regulations Act, were functioning in a very casual manner and disregarding law.
"When we started monitoring their works, they started accusing us of harassing them. But we made it clear that the NGOs must end the casual approach. They must fall in line and follow law.
"No genuine NGO doing legitimate work should be worried as we are making the whole FCRA registration process online and transparent. If an NGO is not doing any wrong, why should it be fearful," he said addressing a seminar on 'International terrorism - how we are being affected'.
FCRA licence of 14,255 NGOs were cancelled between 2006-07 to 2011-12 fiscals. Consequently, registration of 4,138 associations was cancelled in July 2012 and 10,117 in March, 2015.
Recently, registration of several NGOs run by high-profile public figures like Teesta Setalvad were cancelled.
Referring to the killing of suspected LeT terrorist Ishrat Jahan, Rijiju said there was an attempt from the highest level during the UPA government to dilute the case by filing two completely contradictory affidavits in court on whether Ishart was a terrorist or not despite intelligence inputs conclusively saying that she was a LeT terrorist.
Rijiju said the Home ministry is restrictive ministry and cannot disclose its good work but have to take blames for many reasons.
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