The Indian concerns were conveyed by its top business leaders during a meeting with their counterparts under the framework of Japan-India Business Leaders Forum which later presented its report to Modi and Japanese Prime Minister Shinzo Abe.
At the same time, the Japanese side raised issues regarding transfer policy, taxation and the Goods and Services Tax (GST).
"India has taken up some issues of access in Japan," leading Indian industrialist Baba Kalyani, who is the Co-Chair of the Forum, told PTI.
Of the bilateral trade of USD 16.29 billion in 2013-14, the trade deficit was about USD 3 billion and the Indian side is keen to bridge it.
Also Read
At present, India's share is less than 1 per cent of total Japanese pharmaceutical market as Indian pharma companies face non-tariff barriers there.
According to industry experts, the CEPA, which has been in place since 2011, is benefiting Japan more.
Holding out positive prospects for the future of bilateral economic relations, Kalyani said the Japanese businesses are "upbeat" since the Modi government came to power as they feel execution will happen at much faster pace.
"They are more optimistic in investing now," Kalyani said, citing his observation on the basis of interaction with the Japanese business leaders.
Modi was on a visit to Japan from August 30 to September three.