Foreign Secretary S Jaishankar and Japanese Ambassador Kenji Hiramatsu exchanged diplomatic notes, marking operationalisation of the pact, the External Affairs Ministry said.
The civil nuclear cooperation agreement was signed last November during Prime Minister Narendra Modi's visit to Tokyo after years of negotiations.
"This agreement is a reflection of the strategic partnership between India and Japan and will pave the way for enhanced cooperation in energy security and clean energy.
The deal allows Japan to export nuclear technology to India, making it the first non-NPT signatory to have such a deal with Tokyo.
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Japan is a major player in the nuclear energy market and an atomic deal with it will make it easier for US-based nuclear plant makers Westinghouse Electric Corporation and GE Energy Inc to set up atomic plants in India as both these conglomerates have Japanese investments.
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