Wario has set up a committee to investigate the misconduct and it will report its findings by Sept. 30. The Directorate of Criminal Investigation has also been asked to begin a probe.
"There was alleged mismanagement of the facilitation of our athletes and the entire team Kenya ranging from accommodation and travel mishaps, mishandling of the accreditation of the list of participants to the provision of kits that never reached the athletes," Wario told a news conference.
"I do hereby disband the National Olympic Committee with immediate effect and transfer their responsibilities to the Sports Kenya as the interim custodian."
Before the Games, Kenya team captain Wesley Korir berated local Olympic committee officials, saying they needed better management, payment of pending allowances and an immediate end to alleged harassment of athletes by anti-doping officials.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
Francis Paul, NOC-K's secretary general, said his organisation would consult with the International Olympic Committee over Wario's decision.
"We are going to inform the International Olympic Committee to investigate the matter. We shall meet and discuss," he told Reuters.
Despite the problems, Kenya enjoyed its most successful Olympics in Rio, winning six gold medals, six silvers and one bronze, all in track and field.
Korir said on Twitter on Thursday that most Kenyan team members were still in Rio de Janeiro waiting for flights back home and they are staying in a run-down part of the city.
(Writing by George Obulutsa, editing by Ed Osmond)
