Japanese Ambassador Akitaka Saiki said the nuclear disaster following a tsunami sent a "very very serious message" but both the countries will go back to talks to firm up the proposed pact.
"It is not that because of the tsunami, we are going to cancel the talks or postpone it," he said in reply to a question.
Japan and India had started talks for a civil nuclear cooperation agreement last year, aiming at allowing Japanese companies to export atomic power technology and equipment to India.
But there were apprehensions that these negotiations could receive a setback following the radiation scare in Fukushima nuclear power plant after the tsunami struck the country in March 11.
Noting that both India and Japan are currently in the process of strengthening the safety mechanism in nuclear power plants, Saiki said it may take some time to resume the negotiations on the nuclear pact.
"I think the review process both in India and Japan will take some time. We need to ally concerns of our residents and we need to go through the process of persuading our residents living in neighbourhood of nuclear power stations," he said.
Without giving details, he said there are "core issues" which need to be discussed and resolved at the negotiating table."We both know what the core issues are. We will overcome them. We are very very constructive in our approach," he said.