There are fears more corpses could be found as search teams unearthed 17 bodies on Tuesday, with investigators saying children made up the majority of victims of what has been dubbed the "Shakahola Forest Massacre."
Visiting the site on Tuesday, Interior Minister Kithure Kindiki warned that worse could still come.
"We don't know how many more graves, how many more bodies, we are likely to discover," he told reporters, adding the crimes were serious enough to warrant terrorism charges against Nthenge.
He said 34 people had been found alive so far in the vast forest, where police were tipped off about the cult's activities and a crime scene has been established.
"The majority of the bodies exhumed are children," a forensic investigator told AFP on condition of anonymity.
As the fatalities mounted, authorities at the state-run Malindi Sub-County Hospital warned Tuesday that the morgue was running out of space to store the bodies and already operating well over capacity.
"The hospital mortuary has a capacity of 40 bodies," said the hospital's administrator Said Ali, adding that officials had reached out to the Kenya Red Cross for refrigerated containers.
It is believed that some followers of the Good News International Church could still be hiding in the bush around Shakahola and at risk of death if not quickly found.
The Kenya Red Cross said 212 people had been reported missing to its support staff in Malindi, out of which two were reunited with their families.
Hussein Khalid, executive director of the rights group Haki Africa that tipped off the police, urged the authorities to send more rescuers to scour the 325-hectare (800-acre) area of woodland for survivors.
Inspector General of Police Japhet Koome told reporters on Monday that 29 people had been rescued and taken to hospital.
"Each day that passes by there is very high possibility that more are dying," he told AFP. "The horror that we have seen over the last four days is traumatizing. Nothing prepares you for shallow mass graves of children."
Investigators told AFP they found bodies squeezed into shallow pits - with up to six people inside one grave - while others were simply left outside on the ground.
President William Ruto has vowed to take action against rogue pastors like Nthenge "who want to use religion to advance weird, unacceptable ideology," comparing them to terrorists.
As the Kenyan authorities try to uncover the true scale of what is being dubbed the "Shakahola Forest Massacre," questions have emerged about how the cult was able to operate undetected despite Nthenge attracting police attention six years ago.
The televangelist had been arrested in 2017 on charges of "radicalization" after urging families not to send their children to school, saying education was not recognized by the Bible.
Nthenge was arrested again last month and released on bail, according to local media, after two children starved to death in the custody of their parents.
The case is due to be heard on May 2.
The case has prompted calls for tighter control of fringe denominations in a country with a troubling history of self-declared pastors and cults that have dabbled in criminality.