The state has linked the deaths to Pastor Paul Makenzi of Good News International Church and Ezekiel Odero of New Life Prayer Centre.
He said two agents from the media, civil society and the Red Cross will be allowed to access the grave sites in what is seen as a response to public outcry over the whole process.
"As of now treat it as rumours (missing body parts). People who have facts are those on the ground not those in offices," said Kindiki, in response to an affidavit filed in court by the DCI.
An affidavit of Chief Inspector Martin Munene annexed to an application seeking orders to freeze bank accounts of New Life Centre, linked the massacre to human body organ trade.
Munene claimed the postmortem reveals that some of the 112 bodies recovered had missing organs. This is despite pathologists insisting that all bodies were intact.
The DCI officers swore the affidavit in an application seeking orders to freeze Pastor Odero and church bank accounts .
On Friday, Chief Government Pathologist Johansen Oduor said the autopsy report on the 112 corpses ruled out body organ harvesting. The autopsies were conducted at Malindi Sub County Hospital.
He said the victims were either forcefully starved, hit by a blunt object, or strangled to death on different days. Some bodies had severely decomposed.
Yesterday, Kindiki said the state had nothing to hide and that tremendous progress had been made in the investigations expected to lead to arrest of third-tier suspects.
Odero was arrested after the police linked him to Pastor Makenzi, who the state says lured his followers to starve to death to meet Jesus.
Kindiki said 20 more graves were found in the forest and that exhumation and postmortem will take longer.
"Twenty more fresh graves have been identified which means this process will take longer than we anticipated. I can conclude that this was a highly organised crime and the government will unravel it," said Kindiki.
The probe was supervised by Assistant Inspector General of Police Abdhala Komesha. Some 65 people found fasting in the forest were rescued and taken to hospital.
"We have used drones to track movements and disturbance of thickets during the day," said the CS.
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Odero and Makenzi have not been charged despite DPP Noordin Haji's earlier assertions that they will face terrorism and radicalisation charges.
Odero was released on a Sh1.5 million cash bail on Thursday last week after a magistrate dismissed the DPP's application to extend the custodial period by 30 days.
State prosecutor Peter Kiprop asked the court to allow the police to continue holding Odero, saying there was evidence that the deaths that occurred in his church were criminal.
Kiprop said the prosecution was not focusing on gathering evidence to sustain the murder charge against the televangelist.
Meanwhile, Makenzi and 16 others arrested on April 14 are also in custody as the State seeks an extra 90 days for investigations.