Interior CS Kithure Kindiki has said the children in the Shakahola cult may have been subjected to sexual assault.
He said among the leads the security agencies were following, was the sexual abuse of children in the shanties constructed in the 800-acre forest.
"We have some leads that those shanties may have been used probably for sex orgies involving children," Kindiki said.
Speaking when he appeared before the Ad hoc Committee on the Proliferation of Religious Organisations on Friday, the CS regretted that such cruelty may have been done in the name of religion.
On Thursday, Kindiki visited Pastor Paul Mackenzie's shanty in Shakahola Forest where he reportedly stayed during his vocational work.
Mackenzie is accused of leading his followers into believing that if they starved to death, they will meet Jesus.
As of May 25, 241 bodies had been exhumed from the mass graves in Shakahola.
The autopsies done on the first 112 bodies showed that most of the victims died of starvation while others died of asphyxiation.
Chief pathologist Johansen Oduor said the victims, including children, died of strangulation, suffocation and beatings.
So far, 39 people have been arrested in connection with the indoctrinated teachings of Mackenzie.
Those rescued are 91.
On Thursday, Kindiki announced the extension of the curfew at Chakama Ranch.
"There will be no movement at Chakama ranch without the permission of the Kilifi County Commander. The area remains a scene of crime and out of bound from everyone except officers who are working," Kindiki said.
