The man widely considered to be Mungiki's national leader, Mr John Maina Njenga, and 32 others were yesterday charged with being members of an unlawful society.
His prosecution comes more than a year after Narc came to power and signalled its determination to stamp out the movement, some of whose members have been linked to bloody attacks on members of the public.
The court heard that between February 26, 2004, and March Mr Njenga became a member of the society yet he knew or had reasonable cause to believe it was unlawful.
One of 33 suspects with who Mr Njenga had been arrested, Mr Solomon Wanyoike, was not present in court.
Ten other people charged with Mr Njenga faced a different count of intending to commit a felony.
Police claim that on February 26, at a slum behind Riverside Hotel in Nairobi, they were found armed with machettes, swords and clubs.
It is also claimed that the group took an unlawful oath.
The suspects, all young and without the trademark Mungiki dreadlocks, were brought to court at 3pm and the charges were read out immediately.
The suspects were expected to take their pleas in the morning but did not appear before the chief magistrate.
Prosecutor Moses Odoyo said the suspects were a threat to national security and asked that they be remanded in custody.
"Even though we have the suspects in court there are others who are still at large, I fear if they are released on bail they will continue with their activities," said Mr Opondo.
But defence lawyers opposed the application to deny the suspects bail.
The 33 suspects will have spent four nights in custody by Tuesday, when the Chief Magistrate will give his ruling on whether to give them bail or return them to remand.
The state also promised to present Mr Wanyoike, the missing suspect, in court on Monday.