The deal, expected to open the door for Japanese companies to set up nuclear reactors in India, will come into effect once Japan's parliament ratifies it and India was confident of its clearance.
Briefing reporters on the deal, Foreign Secretary S Jaishankar recalled that there were four stages in the Indo-US civil nuclear deal such as signing of 123 agreement in 2007, getting NSG clearance in 2008, finalising the reprocessing pact in 2010 and finally inking the administrative pact in 2015.
He said Japan's sensitivities and concerns were addressed, adding much more emphasis was given on nuclear safety and security.
Asked whether he was confident that Japan's Parliament will ratify the pact, Jaishankar said, "We conclude agreements in the expectation that they are then ratified and implemented. I do not see any reason why that should not be the case in case of Japan."
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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.
"It is very much on the lines of those we signed
earlier," said Jaishankar.
Besides the US, India has signed civil nuclear deal with Russia, South Korea, Mangolia, France, Namibia, Argentina, Canada, Kazakhstan and Australia.
"Japan is a NPT and CTBT signatory. We understand that Japan would have those positions. From our point of view we have a very strong non-proliferation record, very responsible record.
"That is the record which has been basis for international cooperation in civil nuclear energy with us. So while we are not a party to the NPT, there was a broad recognition including by Abe that this is a country which has a very responsible record, truely a worthy partner in nuclear sector," Jaishankar said.
Asked whether there was a termination clause in the pact, he said most of the nuclear cooperation pacts have such provisions.
On whether there was Japan specific features in the agreement, he said he talked about annexures pertaining to reprocessing and some other provisions including change in technical definitions, adding concerns and priorities of the partner countries are incorporated.