Though there was no official word on the reasons for the Japanese side curtailing the visit, the move comes amid increasing tension in the South China Sea region following a UN-backed international tribunal ruling against China's claims over the troubled waters.
Gen Nakatani will hold talks with his counterpart Manohar Parrikar at his South Block office tomorrow afternoon.
The two sides could issue a joint statement after the talks, defence sources said.
The talks will focus on greater defence cooperation, including defence manufacturing.
They had also said Japan would like to further enhance economic cooperation with India and work jointly to enhance regional connectivity.
India and Japan are looking at deepening bilateral defence cooperation amid Tokyo's ongoing tussle with Beijing.
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.
Japanese Prime Minister Shinzo Abe had had told Parrikar that "a strong" India-Japan partnership was not only in the "national interest of the two" but also "important for peace and security in the region".
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