Eric Kiraithe, a national police spokesman, said: "We have things under control and have deployed security forces across the country.
"We assure the public that peace will be restored and all these hooligans brought to book."
The sect accuses a section of the police force of being behind the killings of its members.
Kiraithe denied any police involvement as "totally false accusations".
Since March last year, the Mungiki has been blamed for murdering dozens of people, and for beheading several, mainly in the slum districts of Nairobi and in central Kenya.
The Mungiki sect was once a religious group of dreadlocked youths who embraced traditional rituals, but the authorities say it has evolved into a criminal gang involved in extortion and murder.
Police launched a fierce clampdown on the sect last year resulting in at least 100 deaths.
The unrest came only hours after a new power-sharing cabinet was unveiled in a bid to end Kenya's political crisis since disputed elections in December.
The Mungiki sect, which first emerged in the 1980s, is said to have been initially inspired by the Mau Mau rebellion of the 1950s against British colonial rule.
But since then it is said to have undergone a metamorphosis, with members turning to horrific crimes and now likened to Kenya's version of the Mafia.
A surge in murders and attacks associated with the sect last year prompted a police crackdown. Humans rights groups have condemned what they say are extrajudicial killings by police in its campaign against the Mungiki.