The partnership, which focuses on how to preserve heritage while building smart cities, was signed between Kyoto Mayor Daisaku Kadokawa and India's Ambassador to Japan Deepa Gopalan Wadhwa, ministry of external affairs spokesperson Syed Akbaruddin said.
"Partners in heritage. Kyoto-Varnasi partnership agreement signed in presence of @PMOIndia and PM @abeshinzo in State Guest House," Akbaruddin tweeted.
"Varanasi and Kyoto partner in Smart Heritage Cities prog. Amb Wadhwa & Mayor Kadokawa sign MoU. PM @narendramodi & PM @AbeShinzo witness," he said in a second tweet.
Prime Minister Narendra Modi reached Japan on Saturday on a five-day official visit and was received by his Japanese counterpart Abe in Kyoto.
Earlier, Akbaruddin said that Kyoto, the ancient capital of Japan, had been included in Modi's schedule as it "dovetails into Modi's emphasis on rejuvenation of cities while preserving their cultural heritage." The Hindu holy city of Varanasi in part of the prime minister's Lok Sabha constituency.