A bench headed by Justice H L Dattu refused to grant six more months time as pleaded by the agency and directed it to complete the task within two months.
NGOs have come under judicial scrutiny with the Supreme Court on September 2 asking the CBI to provide details about such registered organisations and their financial statements on a PIL seeking probe into alleged embezzling of funds.
The apex court had expanded the scope of the PIL which was filed in 2011 against an NGO, Hind Swaraj Trust, run by anti-corruption crusader Anna Hazare.
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.