Rift Valley police boss John M'Mbijiwe is among three top officers interdicted by the National Police Service Commission over the fake policeman saga.
The Anti Stock Theft Unit (ASTU) commandant Remi Ngugi and Njoro Officer Commanding Police Division (OCPD) Peter Nthiga have also been sent home.
Mr M'Mbijiwe has been replaced by Levine Mwandi, a deputy commissioner of police.
Mr Ngugi's deputy Solomon Makau takes over as ASTU boss while Mr Nthiga has been replaced by Esau Ochorokodi.
NPSC boss Johnstone Kavuldi said the officers had been adversely mentioned during preliminary investigations.
He said their continued stay in office would interfere with investigations but maintained that the officers were innocent.
Mr Kavuludi said a team had been formed to spearhead the inquiry into the saga.
The team comprises of NPSC commissioners Mary Awuor, a former commandant of the CID training school and Dr Major (rtd) Muiu Mutia, formerly of the Kenya Army.
Others include members drawn from the Public Service Commission, Law Society of Kenya and representatives from the Attorney General and Inspector General of Police offices.
On Monday, Mr M'Mbijiwe and his predecessor Francis Munyambu who worked with the man charged with impersonating a senior police officer were summoned to Nairobi.
The two held meetings with Inspector-General David Kimaiyo and the National Police Service Commission.
Mr Waiganjo was arrested last week for pretending to be a senior superintendent of police but his family maintained that he was appointed to the position by former police commissioner Mathew Iteere.