The matter was raised by visiting Commerce and Industry Minister Anand Sharma with Japanese Foreign Minister Fumio Kishida.
Sharma is on a two-day visit to Tokyo for a comprehensive review of bilateral economic engagement.
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"He (Sharma) flagged concerns of India relating to mounting trade deficit and specially urged for market access for Indian agricultural and marine produce and Indian pharmaceuticals," an official release said.
The Japanese pharma market is projected to touch $100 billion and Indian generics can play a key role in providing affordable healthcare, it said.
India's trade deficit with Japan stood at over $6 billion in 2012-13.
Sharma also called upon Japanese Prime Minister Shinzo Abe and apprised him of the progress made in the implementation of the Delhi Mumbai Industrial Corridor (DMIC) project, which was conceptualised during the 2007 visit of Abe to India.
"Abe expressed satisfaction over the amount of work put into the project and mentioned that Japanese companies are looking forward to partner with India in project implementation," it said.
Japan has already committed $4.5 billion in the first phase of project implementation, it said adding India has committed an equal amount for development of trunk infrastructure for creation of new industrial townships along the corridor.
Japan has taken 26% equity in the project.
The CEO of Japan Bank of International Cooperation (JBIC) Hiroshi Watanabe also met Sharma and assured him of full financial support for the project and other infrastructure projects in India.
Sharma also met the Japanese Minister of Economy Trade and Industry Toshimitsu Motegi.
Besides, he attended the India Investment Roundtable meeting, asking Japanese business community to explore business opportunities in India.
Sharma's visit comes ahead of Prime Minister Manmohan Singh's visit to Tokyo, the release added.
The roundtable meeting was organised by the ministry and CII.
"The demand for electronic hardware in India is increasing rapidly and Japan's support in meeting this demand would be important," CII said in a statement.
India's imports from Japan, with which it implemented a comprehensive free trade agreement in 2011, increased by over 3% to $12.5 billion last fiscal.
On the other hand, the country's exports to Japan declined to $6.26 billion during the last fiscal from $6.32 billion in 2011-12.