Naruhito will have the polyp removed in a noninvasive, endoscopic operation at the University of Tokyo Hospital on June 6, said Imperial Household Agency spokesman Yasuo Moriyama.
In March, Palace doctors found the polyp in Naruhito's duodenum, the first section of the small intestine, when he had a regular health check.
Palace doctors have decided to have Naruhito's polyp removed at a larger hospital with better medical equipment and personnel than the Imperial Household Hospital, given that his polyp is a rare kind in the duodenum that will need caution and post-surgical care, Moriyama said.
After the operation, the 47-year-old prince is expected to remain in the hospital for about one week and then recuperate at home for another week. His wife, Crown Princess Masako, is still recuperating from a form of depression. She withdrew from virtually all public duties four years ago after being diagnosed.