On the first full day of his five-day trip to Japan aimed at boosting economic and security ties, Modi also exchanged notes on heritage conservation with Kyoto Mayor Daisaku Kadokawa, showing him a detailed map of Varanasi, the Hindu holy city he represents in the Lok Sabha.
Modi, who arrived in Kyoto Saturday and was received by his Japanese counterpart Shinzo Abe, began Sunday by visiting the Toji and Kinkaku-ji temples.
Dressed in a white kurta pyjama and bandhgala, Modi first went to the Toji temple with Abe, who flew down to Kyoto specially to receive the Indian leader.
Abe guided Modi around the Toji temple to take a look at its Buddhist statues and five-storied pagoda, which is a national treasure, Kyodo news agency reported. Modi also walked through the temple premises.
Abe said: "Looking at statutes of Buddha, we were reminded of the deep historical ties between Japan and India."
The chief monk of the 57 meters tall eighth century shrine explained to him the features of the temple, a Unesco Heritage site.
The two prime ministers "rekindle ancient India-Japan civilisational bonds with visit to Toji temple", an external affairs ministry spokesman tweeted.
Modi then went to the Kinkaku-ji temple, which was built in 1397 and where he interacted with a number of visitors who greeted him enthusiastically, an Indian official statement said.
To its 83-year-old head priest Yasu Nagamori, Modi said: "I am Modi and you are Mori."
At Kyoto University, Modi met stem cell pioneer Shinya Yamanaka, the Nobel winner in 2012.
They discussed the "possibilities of sickle cell anaemia cure" and "prospects of cooperation among Indian and Japanese institutes", tweeted the external affairs ministry.
"The prime minister expressed concern over the prevalence of sickle cell anaemia, especially among the tribal communities across India."
Sickling decreases the cells' flexibility and results in a risk of various life threatening complications. It mostly occurs in regions where malaria is rampant.
"The prime minister urged Yamanaka to work towards a cure for this," the statement said.
Yamanaka said there were currently no Indian researchers at his institute, the Centre for iPS Cell Research and Application, and "he would like Indian scientists to conduct research at the institute".
Mayor Kadokawa briefed Modi about "green, smart and modern yet historic Kyoto". Kyoto is home to about 1.5 million people. Modi discussed with him Varanasi, which the BJP veteran is determined to turn into a modern city while retaining its ancient and religious roots.
Changing later into a dark mustard kurta and a light brown bandhgala, the Indian leader attended a luncheon hosted by the Kyoto Buddhist Association, met the governor of Kyoto Prefecture, Keiji Yamada, and held talks with the CEO of Nidec Corp, Shigenobu Nagamari.
India's ambassador to Japan, Deepa Gopalan Wadhwa, was also present.
Abe said that he was happy Modi toured Kyoto, the country's ancient capital. He said he had valuable exchanges with Modi on cultural ties and international affairs.
He said he looked forward to seeing Modi in Tokyo Monday.
Modi and Abe met Saturday for about 90 minutes. The meeting was described by Indian officials as "exceptionally warm and friendly". Modi attended an unofficial dinner hosted by Abe at the Kyoto State Guest House.
Within hours of Modi's arrival, a partnership accord was signed between Varanasi and Kyoto.
This is Modi's first bilateral sojourn outside South Asia since taking office in May.