Modi and Abe reaffirmed their commitment to work together for India to become a full member in multilateral export control regimes such as the Nuclear Suppliers Group (NSG), Wassenaar Arrangement and the Australia Group.
Abe also welcomed India's accession to the Missile Technology Control Regime (MTCR) and the Hague Code of Conduct against Ballistic Missile Proliferation (HCOC).
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India has applied for a membership in the 48-member NSG in May 2016, but is facing stiff opposition, primarily from China.
"They (the two prime ministers) looked forward to a working group to strengthen bilateral cooperation in this field and reiterated their shared view that the agreement reflects a new level of mutual confidence and strategic partnership in the cause of clean energy, economic development and a peaceful and secure world," according to a joint statement, released after the delegation level talks.
Referring to the nuclear pact, Modi, in a media statement after the delegation level talks with Abe, said it would open a new chapter in cooperation in the clean energy sector between the two countries.
"We had signed a historic pact for peaceful use of nuclear energy during my visit to Japan last year. I am whole-heartedly thanking Japan's parliament, its people and particularly Prime Minister Abe for its ratification," Modi said.
A civil nuclear pact is important for foreign players building atomic reactors in the country. The pact would enable them to procure high-end equipment from Japan.
"We really see Japan as a significant partner in many of our nuclear power projects which we will doing with other countries," Foreign Secretary S Jaishankar told reporters at a media briefing.
The nuclear cooperation agreement between India and Japan was signed in November 2016. The agreement came into force in July this year after it was ratified by the Diet of Japan.