A bench comprising Chief Justice H L Dattu and Justice A K Sikri asked the probe agency to write to the chief secretaries of the states which are not providing the details despite the court order in this regard.
"We will direct the CBI to take appropriate steps," the bench said during the brief hearing of the 2011 PIL filed by lawyer M L Sharma.
The counsel for the CBI informed the court that various states like Arunachal Pradesh, Delhi and Punjab have so far not responded to its queries.
The agency, however, had submitted that most of the NGOs are not filing IT returns.
More From This Section
It had said that Gujarat and Tamil Nadu have not given information about the NGOs working in their states and Andhra Pradesh, Bihar, Haryana, Madhya Pradesh, West Bengal, Odisha and Maharashtra provided only partial inputs.
NGOs have come under judicial scrutiny with the Supreme Court on September 2, 2013 asking the CBI to provide details about such registered organisations and their financial statements on a PIL seeking probe into alleged embezzlement of funds.
Earlier, the agency had expressed difficulty in probing and collecting information on NGOs and had pleaded that the task be handed over to states, but the plea was summarily rejected by the court which directed the agency to comply with its order.
"If CBI can probe murder cases then why not probe against NGOs? You can do so many things, you do it also," the bench had said.