Bishop Eliud said that he was taking up the role at a time when corruption was perceived to be high.
He also said that he would need the cooperation of other state agencies to help the institution's efforts to eliminate corruption. He warned that people should stop stealing money "from today".
Attorney General Githu Muigai praised Mr Wabukala, saying "there are no good hands to fight this war than the hands of a man of God".
Previous anti-graft chiefs have found their intentions frustrated and have been forced to resign after political pressure or after themselves being accused of facilitating corruption.