North Koreans are banned from entering Japan as part of sanctions imposed for its missile and nuclear tests.
Kim Il Guk, who also serves as the president of the North's Olympic committee, will travel to Japan to take part in the Association of National Olympic Committees (ANOC) General Assembly on Wednesday and Thursday.
"International sports and the Olympics charter share this notion of no discrimination against any nationalities," Japan's Chief Cabinet Secretary Yoshihide Suga said at his regular briefing on Tuesday.
"On the basis of that, it is an exception that we have allowed minister Kim Il Guk, who is planning on coming to this week’s General Assembly. We have allowed him to enter the country as an exception."
This is not the first time Japan has waived the ban in the name of sports.
In February 2017, North Korean athletes and officials were granted permission to enter the country for the Asian Winter Games in Sapporo.
North Korea also plans to attend the 2020 Olympic Games in Tokyo.
(Reporting by Jack Tarrant; Editing by Peter Rutherford)
