The charges, announced during an appearance before a court in the southeastern city of Mombasa, are the first to be brought against Mackenzie, who was arrested last April after the bodies were first discovered.
Mackenzie and his co-defendants denied the charges during their appearance before the judge, Joe Omido. They are due back in court on Feb 8 for a bond hearing.
Authorities say Mackenzie, the head of the Good News International Church, ordered his followers to starve themselves and their children to death so that they could go to heaven before the world ended.
A lawyer for Mackenzie has said the self-styled pastor is cooperating with the investigation.
A judge in a different court, in the coastal town of Malindi, ordered on Wednesday that Mackenzie and 30 of his associates be taken for mental health evaluations before being charged with murder in connection with 191 of the deaths.
Prosecutors in Mombasa and Malindi say they will also charge the 95 people on counts of manslaughter and torture.
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