Church-based groups are under the scanner in southern Tamil Nadu after the Home Ministry scraps the licences of three NGOs for diverting funds to the protest movement against the Kudankulam nuclear plant.

The Union Home Ministry has cancelled the licences of three non-govermental organisations operating in southern Tamil Nadu on the charge that they diverted funds for the protests against the Kudankula Nuclear Power Plant.

The action follows Prime Minister Manmohan Singh's comments to Science magazine that suggested that US non-governmental organisations were behind the agitation, which has stalled work on the nuclear plant in power-starved Tamil Nadu. The first of the two 1000-MW reactors, being built with Russian help, was to have been de commissioned in December 2011, but work on the project has been suspended since August 2011 after the protests intesified.

Singh's comments had whipped up a controversy, with the leader of the protest movement SP Udayakamar challenging the Prime Minister to prove his charge - or resign. (Watch the debate on CNN-IBN here.)

Minister of State in the Prime Minister's Office V Narayanasamy on Friday confirmed the action against the three NGOs, but did not disclose their names. But earlier this month, Narayanasamy had alleged that NGOs administered by Tuticorin church leader, Bishop Yvon Ambroise, had received foreign funds to the tune of Rs 54 crore. Ambroise has been active in mobilising popular support for the anti-nuclear protests.

Narayanasamy also alleged then that a third NGO run by Udayakumar, who heads the People's Movement Against Nuclear Energy, had received Rs 1.5 crore in foreign funds. He had said then that if the NGOs were not shown to have maintained proper accounts for the expenditure on these amounts, the Home Ministry would initiate stringent action against them for violation of the Foreign Contribution (Regulation) Act (FCRA).

The NGOs associated with Ambroise are the Tuticorin Diocese Association (TDA) and the Tuticorin Multipurpose Social Service Society (TMSSS). Indian Express reports that both these NGOs had FCRA clearance until last year, but their names have now been removed from the home ministry website listing over 42,000 NGOs having FCRA clearance.

The Home Ministry notes on its website that TMSSS received Rs 42 crore from abroad in the last five years (details here) for rural development work, and that TDA received Rs 23 crore.

Many other Christian organistions, including People's Education for Action and Liberation (PEAL) and Good Vision, are also under the Home Ministry scanner for alleged funding of the anti-nuclear protest movement.

Udayakumar told CNN-IBN that his organisation had not received even a single rupee from abroad. "I am willing to undergo capital punishment if the allegation that I received foreign funding is proved," he said.

In his interview to Science magazine (report here), Singh had said that that foreign NGOs did not appreciate India’s need to make use of high-technology like nuclear energy or genetically-engineered crops for the sake of development.

“You know... what is happening in Kudankulam," he told Pallava Bagla. "The atomic energy programme has got into difficulties because these NGOs, mostly I think based in the United States, don’t appreciate our country to increase the energy supply,” Singh said.

Singh also noted that NGOs based in the US and in Scandinavia had effectively blocked the commercialisation of Bt brinjal in 2010. “There are NGOs, often funded from the United States and the Scandinavian countries, which are not fully appreciative of the development challenges that our country faces,” Singh said.