Ten more bodies were exhumed on Friday from Shakahola Forest land linked to Pastor Paul Mackenzie, bringing the death toll to 336.
Coast Regional Commissioner Rhoda Onyancha confirmed that the government had suspended the third phase of exhumations, which had been ongoing for two weeks.
This is to pave the way for autopsies on the bodies recovered during the third phase of the exercise.
Ms Onyancha noted that the dates on which the post-mortem would be conducted would be announced soon.
However, no rescues were made during the latest exercise. So far, 95 people have been rescued and 36 arrested.
Interior Cabinet Secretary Kithure Kindiki has admitted that the government slept on the job, leading to the killing of more than 300 Kenyans by a doomsday cult in Shakahola Forest, Kilifi County.
Speaking in Lamu on Friday at the end of a three-day tour of the county, Prof Kindiki insisted that the Shakahola cult massacre would not have happened if security agencies, community and religious leaders had been vigilant.
Similar to President William Ruto's move last month, CS Kindiki went on to apologise to Kenyans for the failure of both the past and present governments to prevent the deaths of hundreds of innocent citizens at the hands of preacher Paul Mackenzie and his cohorts who hid in religion.
Prof Kindiki warned that there will be no more transfers for security officers who fail to do their jobs, but that he will ensure that such officers are sacked.
"It is unfortunate to see criminals hiding in religion. We have people masquerading as Muslim and Christian clerics and pastors. For example, the Shakahola massacre. In fact, I would like to apologise to Kenyans today, as did our President. It's obvious that there was laxity in both the previous and current government regimes that unfortunately led to the death of many citizens in Shakahola. I do not take this lightly. This problem started many years ago. If our security agencies, religious leaders and the community had been vigilant, the Shakahola issue wouldn't have reached this level," said the CS.
He urged security agencies in Lamu and the country at large to work closely with local communities in their daily operations to effectively tackle terrorism, radicalisation, drugs and other crimes.