Both the nations termed the deal as "historic".
"We strongly register our protest against this disastrous deal. Japan and India should cooperate on renewable technologies," said a statement issued by the CNDP.
"India-Japan nuclear agreement would unleash destruction in India. It effectively means displacement and loss of livelihoods for the farmers and fisherfolk, environmental damage and radiation hazard due to unsafe and untested reactors, disruption of the non-proliferation regime and nuclear arms race in South Asia," the statement added.
The CNDP is an all India network of over 200 organisations, including grassroots groups, mass movements, advocacy organisations and individuals.
Formed in November 2000, CNDP's main agenda has been to put pressure on both India and Pakistan to rollback their nuclear weapons programmes.
CNDP strongly focusses on the issue of regional and global disarmament.
CNDP works to raise mass awareness through programmes in schools and colleges, publications, audio and visual materials, campaigning and lobbying at various levels.
The deal was signed during Prime Minister Narendra Modi's visit to Tokyo on Friday.
The agreement will allow Japan to supply nuclear reactors, fuel and technology to India for civilian use.
Read the full statement of CNDP below:
The Indian PM is in Tokyo today and reportedly he will finalise the nuclear supply agreement with Japan.
This agreement with Japan is the remaining piece of the Indo-US nuclear deal, ensuring supply of reactor equipments from Japan which are essential for the American and French nuclear plants being set up in India.
In Maharashtra's Jaitapur, this would fast-track the construction of world's largest nuclear power plant, consisting of 6 EPR reactors whose safety has been questioned by the French nuclear safety regulator ASN itself.
In Andhra Pradesh's Kovvada, it would aid American-imported reactors of GE-Hitachi.
The deal would unleash misery on the most vulnerable people in India, by aiding an anachronistic nuclear expansion.
India is among very few countries in the world today to embark on such massive expansion after Fukushima.
The Indian government has been bulldozing everything that stands in the way of implementing new reactors - undermining and diluting safety norms, curtailing transparency on nuclear-related pushing through environmental clearances at gun-point, neglecting the adverse economics of these projects, brutally crushing grassroots democratic dissent, and trying to exempt the nuclear suppliers from liability in the event of any accident.
The govt has labelled peaceful anti-nuclear agitators as anti-nationals, unleashing violence on innocent farmers, fisher folk, women and children.
The deal would become the final seal of legitimacy for India's nuclear weapons and will further fuel the nuclear arms race in South Asia.
An import-based civilian nuclear industry would free up India's domestic resources exclusively for weapons.
Concerned people in both India and Japan have been opposed to the nuclear agreement.
Protests against this agreement are also happening in Jaitapur, Kovvada, Gorakhpur, Mumbai, Kolkata, Bangalore and several cities of Japan.
Solidarity messages have been sent by concerned people in other countries to Indian and Japanese embassies.