Akihito, accompanied by his wife, Empress Michiko, paid respects at Koma Shrine in the town of Hidaka as part of a two-day private study trip to the region, palace officials said. Akihito has made short trips to small Japanese towns to learn about local history, traditions and culture for more than a decade.
Nearly 1,800 Koreans settled in the area in the 7th century, and the shrine was established to commemorate their leader.
Akihito, 83, listened intently, sometimes asking questions, as the 60th head priest escorted the couple and explained the history of the shrine and the region.
The emperor and the empress also walked in a nearby park filled with red spider lilies in full bloom.
Preparations for Akihito's abdication are underway after he expressed a wish last year to retire.