The home ministry ordered probe against four NGOs on Tuesday for alleged diversion of foreign funds to fuel protests against the Kudankulam nuclear power project.
But the ministry did not cancel their registration, as was initially claimed, nor did it name them.
As HT reported on Tuesday, government sources confirmed that the ministry asked the CBI to probe two NGOs where the suspected amount of diverted funds exceeded Rs 1 crore, while the other two will be handled by the Tamil Nadu crime branch.
Sources said the communication was sent in the first week of February, long before Prime Minister Manmohan Singh's remark on foreign-funded NGOs channelling money into the protests. Besides, accounts of some more NGOs operating in Tamil Nadu's coastal belt were still being audited.
Home ministry officials said the claims made by some central ministers that the licences of the NGOs had been cancelled were inaccurate.
"There is a procedure to be followed for cancelling the registration of an NGO. That stage has not been reached yet," said an official.
As Hindustan Times reported first on February 25, the home ministry only froze the foreign contribution accounts of the NGOs because of accounting loopholes.
That's why home minister P Chidambaram declared on February 4 that the Centre was probing the flow of funds received by anti-project activists.
Home secretary RK Singh confirmed that the Centre had directed agencies to register cases for violating the Foreign Contribution Regulation Act. But there was no confirmation if cases had been registered.
"We need the Tamil Nadu government's consent before we can register the case," a CBI official in Delhi said, acknowledging that proving the charge of diversion of funds in court would be a near-impossible task.
It will require the CBI and the crime branch to build a money trail to establish that foreign funds - meant for the stated charitable purposes, and not money generated through local or domestic contributions - were spent on protesters.