Magistrate Yusuf Shikanda said at a hearing in the port city of Mombasa that Mackenzie and 17 other people detained in connection with the mass deaths would not be granted bail because of concerns that their release would jeopardize investigations.
"Being aware of the respondents' right to be presumed innocent until the contrary is proved, I find that there is reasonable suspicion that the respondents may have committed the offences under investigation," Shikanda said.
The death toll has climbed to 133, and hundreds of people are still reported missing. Authorities continue to search for human remains in shallow graves scattered throughout a forest where Mackenzie's followers were living.
Wycliffe Makasembo, a lawyer for Mackenzie and his wife, who is also detained, said he would appeal against the decision.
"The ruling was not within the law. It violates the constitutional rights of our clients," Makasembo told Reuters.
Mackenzie was arrested earlier this year on suspicion of the murder of two children by starvation and suffocation, but was then released on bail.
Relatives of his adherents say that after he was freed, he returned to Shakahola forest and brought forward his predicted world's end date - which had previously fallen in August - to April 15.
Mackenzie surrendered to police on April 14 after police first raided the forest where the Good News International Church was based, rescuing 15 people who had been starving themselves.
In recent days, allegations of organ harvesting from those who starved have been raised.