During the visit, greater defence cooperation including defence manufacturing would be a focus of discussion here with the top civil and military leadership besides the issue in Asia Pacific region.
Gen Nakatani will hold delegation level talk with Defence Minister Manohar Parrikar on July 14.
During Parrikar's visit to Japan last year, Japanese leaders had emphasised on the commonality of strategic interests between the two countries and conveyed Japan's desire to enhance bilateral defence and security cooperation including in the field of maritime security.
India and Japan are looking at deepening bilateral defence cooperation amid Tokyo's ongoing tussle with Beijing.
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Japan has been witnessing conflict with China over control of private islands in South China sea. A territorial dispute even exists between China and Japan over the Senkaku Islands, which Beijing refers to as the Diaoyu Islands.
India considers relations with Japan very important, which is evident from the fact that Parrikar chose Japan as the first country to visit after assuming office of Defence Minister.