Court documents filed on Monday said that some of the corpses had their organs removed, with police alleging that the suspects were engaged in forced harvesting of body parts.
"Post mortem reports have established missing organs in some of the bodies of victims who have been exhumed," chief inspector Martin Munene said in an affidavit filed to a Nairobi court.
It is "believed that trade on human body organs has been well coordinated involving several players," he said, giving no details about the suspected trafficking.
Munene said that Ezekiel Odero, a high-profile televangelist who was arrested last month in connection with the same case and granted bail on Thursday, had received "huge cash transactions," allegedly from Mackenzie's followers who sold their property at the cult leader's bidding.
The Nairobi court ordered the authorities to freeze more than 20 bank accounts belonging to Odero for 30 days.
A total of 112 people have so far been confirmed dead, Interior Minister Kithure Kindiki said Tuesday after arriving in Malindi to supervise the resumption of exhumations, which were suspended last week because of bad weather.
"Search and rescue efforts for persons suspected to be holed up in the thickets and bushes have been going on," Kindiki said.
The discovery of mass graves last month near the Indian Ocean coastal town of Malindi has stunned the deeply religious Christian-majority country in what has been dubbed the "Shakahola forest massacre."
Police believe most of the bodies belong to followers of self-styled pastor Paul Nthenge Mackenzie who is accused of ordering them to starve to death "to meet Jesus."
While starvation appears to be the main cause of death, some of the victims -- including children - were strangled, beaten, or suffocated, according to the chief government pathologist Johansen Oduor.
Questions have been raised about how Mackenzie managed to evade law enforcement despite a history of extremism and previous legal cases.
The former taxi driver turned himself in on April 14 after police acting on a tip-off first entered Shakahola forest, where some 30 mass graves have now been found.
Prosecutors are asking to hold the father of seven, who founded the Good News International Church in 2003, for another 90 days until investigations are completed.
Senior principal magistrate Yusuf Shikanda said he would rule on the request on Wednesday.