A joint statement issued at the end of exhaustive talks between Singh and Abe said the two Prime Ministers reaffirmed the importance of civil nuclear cooperation between the two countries, while recognising that nuclear safety is a priority for both governments.
"In this context, they directed their officials to accelerate the negotiations of an Agreement for Cooperation in the Peaceful Uses of Nuclear Energy towards an early conclusion," it said.
Japan is the only country in the world to have faced nuclear attacks.
Negotiations for the civil nuclear cooperation agreement have not made much headway since Japan was struck by Fukushima nuclear disaster in March, 2011.
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While Japan has backed the Indo-US nuclear deal and the exemptions given to India from international technology sanctions, successive governments in Tokyo have found the going tough in garnering political support for it in the face of stiff opposition from the non-proliferation lobby here.
Terming Japan as a partner, Singh said that at a time of global uncertainties, change and challenges, India and Japan are "natural and indispensable partners for advancing prosperity in our two countries and for a peaceful, stable, cooperative and prosperous future for the Asia-Pacific and Indian Ocean regions".
The remarks came amidst flexing of muscles by China in the South China Sea and East China Sea.
China has in the recent past used its naval ships and aircraft to intimidate neighbouring countries including Japan which are in dispute with Beijing over maritime rights.