Singh, accompanied by his wife Gursharan Kaur, was accorded a red carpet welcome upon his arrival here.
Singh will hold exhaustive talks with his Japanese counterpart Shinzo Abe on Wednesday on the entire gamut of bilateral ties with special focus on giving boost to cooperation in defence, economic, energy and other areas.
"I look forward to further cementing our ties with Japan," Singh said in a statement on his arrival.
"In all areas, there is enormous potential for widening and strengthening our relations with Japan."
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He said that the people of India have "fondness" for the people of Japan.
Singh's visit, originally scheduled for November last year, was postponed following the announcement of general elections in Japan in December.
Meanwhile, reacting to reports that there are issues in Japan on a bilateral civilian nuclear deal with India, official sources said, "India is quite happy to proceed at the pace determined by the Japanese side."
"When Japan is keen to see that whatever it does is in the direction of strengthening non-proliferation regime, India's own view is that civilian nuclear energy cooperation with Japan will only further strengthen non-proliferation regime."
The sources also dismissed reports of India going slow on ties with Japan so as not to annoy China.