Singapore enjoys close ties with Japan not only at the national level, but also with its various prefectures, visiting President Tony Tan Keng Yam said in Japan's ancient capital last night.

Dr Tan arrived in Kyoto by the shinkansen bullet train yesterday after spending the first four days of his nine-day state visit in Tokyo.

His visit comes as the two countries mark 50 years of diplomatic ties, and Dr Tan said at the welcome ceremony at the Kyoto State Guest House: "The links between Singapore and Japan, and in fact Singapore and the various prefectures, continue to strengthen with time."

The guest house is one such example, Dr Tan said. It was built in 2005 by Japanese architectural firm Nikken Sekkei, which was part of a team that was awarded the concept master plan for Singapore's Rail Corridor last year.

Paved cycling paths and sheltered rest areas, event spaces and rainforest viewing platforms all feature in the winning plan, which Nikken Sekkei conceptualised with Singaporean landscape firm Tierra Design.

Dr Tan also pointed to the five- year agreement between the business schools of Singapore Management University and Kyoto University, inked on Thursday, as another example.

The pact furthers academic collaboration through student and faculty exchange, as well as joint research and initiatives.

It is the second agreement between the two universities. The first, involving their economics schools, was signed in August.

"This is the latest in a series of collaborations between our universities, enabling our students and scholars to learn from and work with each other, and establishing friendships between our younger generations," Dr Tan said.

Kyoto Prefecture Governor Keiji Yamada, in his remarks, noted the strong interest among Singaporeans in the historic city, while also expressing his "valuable memory" of having hosted the late President S R Nathan in Kyoto when he was in Japan for a state visit in 2009.

Dr Tan was treated to imperial court music last night, and will attend a tea ceremony today with Dr Genshitsu Sen, a grand master of the Urasenke tea ceremony school.

"Kyoto was the capital of Japan for more than 1,000 years, and has contributed greatly to the development of various traditional arts," he said.