The move was announced by sports minister Amina Mohamed, who said a preliminary investigation into the soccer federation by her department had shown it was unable to properly account for money given to it by the government.
Mohamed said police and anti-corruption authorities in Kenya should now carry out further investigations and decide if there should be criminal prosecutions.
The decision to remove all elected officials at the federation and replace them with a caretaker committee will not affect Kenya's international matches, the sports ministry said.
But that may still happen if world body FIFA becomes involved. FIFA does not allow governments to interfere in the running of national federations and Kenya risks being banned from international soccer.
Kenya was due to play Uganda in a World Cup qualifier later Thursday, although Kenya has already been eliminated and cannot qualify for next year's tournament in Qatar.
Kenya also failed to qualify for the upcoming African Cup of Nations in Cameroon in January and February.
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