Ise Shrine is dedicated to a legendary ancestress of the Imperial family. The couple's visit is part of a series of rituals for the abdication.
When they arrived at the local station they were greeted by throngs of well-wishers. "It's such a pleasure for me to see the Emperor and Empress before the end of his reign," said one person who had made come to see the couple. "I saw them for the first time. I'm moved to tears," said another.
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The couple has attached great importance to meeting members of the public across the country.
In May 1989, they chose Tokushima Prefecture for their first visit since the ascension to the throne.
In the first 15 years of the Heisei era, they traveled to all 47 prefectures. Two years ago they completed the second round. Their travels have taken them from the northern Cape Soya in Hokkaido to the westernmost island, Yonaguni-jima, in Okinawa prefecture.
During the trips, they spent time with people struggling to get by, consoling them with warm words.
On a private trip four years ago, they visited the Kitaharao district of Miyagi Prefecture. The name Kitaharao means North of Palau, because many of the residents were immigrants from the Pacific island nation, where fierce fighting occurred during World War Two.
Their trip came two months after the Imperial couple's visit to Palau to pay their respects to the war dead. They spoke to the elderly of Kitaharao, who had moved there as children. One woman cried when they told her they understand what she had gone through.
Three years ago, the Emperor issued a video message reflecting on his visits.
He said: "I have felt that my travels to various places throughout Japan in particular, to remote places and islands, are important acts of the Emperor as the symbol of the state and I have carried them out in that spirit.
With this awareness I was able to carry out the most important duties of the Emperor, to always think of the people and pray for the people, with deep respect and love for the people. That, I feel, has been a great blessing."
Emperor Akihito will relinquish the throne in less than two weeks, but his connection with people across Japan will endure.