His cousin, who asked for anonymity for fear of police reprisals, said Kamunya was arrested in the presence of his wife and four children.
The Mungiki gang is blamed for the deaths of 15 police officers between April and June and 27 civilians this year. Kamunya has been on the run since April, when police issued an arrest warrant for him. Two other men have since been arrested.
Kamunya is the brother Maina Njenga, the former leader of the banned sect who was jailed in June for five years for illegal possession of arms.
Members of the sect were blamed for dozens of killings, with some of the victims beheaded and their body parts strewn in bushes mainly in Kenya's central province.
Police responded by killing scores of Mungiki adherents.
Kiraithe said: "We want to ensure that they [Mungiki] do not regroup again."
Once a pseudo-religious group of dreadlocked youths, who embraced rituals such as female circumcision, the Mungiki has fragmented into a criminal gang, notorious for activities such as extortion, murder, and harassment of women.
It drew thousands of unemployed youths from Kenya's largest Kikuyu tribe. Formed in the late 1980s, Mungiki, meaning multitude in the Kikuyu language, has drawn its resources from extortion and operated openly until it was banned in 2002.