The two countries had reached a broad agreement for cooperation in civil nuclear energy sector during Abe's visit to India in December last year, but the deal was yet to be signed as some issues were yet to be worked out.
"A landmark deal for a cleaner, greener world! PM @narendramodi and PM @AbeShinzo witness exchange of the landmark Civil Nuclear Agreement," External Affairs Ministry spokesman Vikas Swarup tweeted today.
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The deal would allow Japan to export nuclear technology to India, making it the first non-NPT signatory to have such a deal with Tokyo. It would also cement the bilateral economic and security ties as the two countries warm up to counter an assertive China.
There was political resistance in Japan - the only country to suffer atomic bombings during World War II - against a nuclear deal with India, particularly after the disaster at the Fukushima Nuclear Power Plant in 2011.
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.
Other nations who have signed civil nuclear deal with India include the US, Russia, South Korea, Mangolia, France, Namibia, Argentina, Canada, Kazakhstan and Australia.