The team drew with Malawi in Nairobi on June 2 and lost to Namibia eight days later in two qualifying matches for the 2014 World Cup in Brazil.
Kenya were then beaten 1-0 by Togo, ending their hopes of reaching the finals of the 2013 Nations Cup.
"The national executive committee held a meeting today and resolved to disband the entire technical staff with immediate effect," said Football Kenya Federation (FKF) chairman Sam Nyamweya in a statement.
"Francis Kimanzi has now been appointed acting technical director to replace Patrick Naggi who becomes FKF executive officer."
