Twelve detectives, drawn from Central Police Station and the Flying Squad, grabbed Mr Ibrahim Ndura Waruinge from a police cell and ordered him to take them to his rented house in the outskirts of Ngong town.
The officers, who were armed with AK-47 rifles and pistols, drove to Mr Waruinge's home in four cars and thoroughly searched all the rooms and stores for weapons and the sect's literature.
While some of the officers were ransacking the six-bedroomed house, others kept vigil outside, though the Mungiki followers did not make an appearance as was feared. The operation ended peacefully.
Only his wife, Serina Muthoni, two sisters and four relatives were at the upmarket home.
After the search was over, Mr Waruinge was put in one of the police cars and driven away.
The officers took away Mr Waruinge's Mungiki life membership certificate, 30 photographs of his followers, documents related to the organisation, its bank account and insurance, and a booklet on the Goldenberg International, which is owned by tycoon Paul (Kamlesh) Pattni.
Two hours after the raid, Police Commissioner Philemon Abong'o said they were concerned by Mr Waruinge's claims that Mungiki had recruited and administered oath to more than 6,000 regular police and 1,500 Criminal Investigations Department officers.
In a statement, he assured Kenyans that they were safe from the sect, adding that action would be taken against Mr Waruinge once investigations are complete.
For some time, the Mungiki leader had claimed that the sect's bank account had more than Sh800 million and boasted that he had recruited thousands of members from the police and military.
Mr Waruinge was arrested on Monday after daring the police and announcing that Mungiki followers would take over all matatu routes in the country.
For the past year, Mungiki and Kamjesh gangs have waged street battles over the control of matatu routes. About 15 people have been hacked to death in Dandora after the rival gangs fought.
Last Thursday, Mr Muathe ordered a crackdown on the gangs.