Sports Minister Hassan Wario had ordered that NOCK be disbanded in August, saying the body had not arranged adequate accommodation and travel for the Olympic team in Rio de Janeiro, and had also mishandled other issues.
On Monday, a High Court quashed that order.
"The ministry will abide by the decision of the court," Sports Ministry spokesman Richard Abura said, adding NOCK had until March to hold elections for senior posts under rules agreed by the government and the International Olympic Committee (IOC).
"The ministry knows that (the) International Olympic Committee charter does not allow government interference with NOCK," he said.
Despite problems in the build up to Rio, the East African nation enjoyed its most successful Olympics, winning six gold medals, six silvers and one bronze, all in track and field.
Kenya, renowned for its middle and long-distance runners, was almost barred form the Games because of a series of doping scandals, but avoided the sanction at the last minute after the government passed legislation to comply with anti-doping codes.
(Reporting by Humphrey Malalo and Isaack Omulo; Writing by Clement Uwiringiyimana; Editing by Edmund Blair and Ken Ferris)
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