"Most of them had features of starvation," chief government pathologist Johansen Oduor said after the autopsies took place in a hospital morgue at the town of Malindi.
"We saw features of people who have not eaten -- there was no food in the stomach, the layer of fat was very small," he said.
"We have had a look at all their bodies and all their organs were intact. None was missing so far."
But, Oduor added, "From what we are hearing, there was some indication that they were being smothered, that can be one of the causes of asphyxiation. It was in two children. "
In a case that erupted last month, horrifying a deeply religious nation, cult leader Paul Mackenzie Nthenge is accused of urging followers to find God through starvation.
The provisional death toll stands at 109, which includes a small number of people who were found alive but died on their way to hospital.
Mass graves in the nearby Shakahola forest have revealed scores of dead, most of them children.
"The process of exhumation was temporarily stopped because the experts advised us (that) when it is raining, that process cannot continue," Kindiki said.
Paul Mackenzie Nthenge, a former taxi driver who created a Christian-based cult called the Good News International Church, is accused of telling followers that starvation offered a path to God.
But Kindiki said Friday that preliminary reports suggested "that some of the victims may not have died of starvation. There were other methods used, including hurting them."
The discovery of the bodies deeply shocked Kenya - an impact amplified last week by the announcement that a prominent televangelist would face charges over the "mass killing" of his supporters.
Ezekiel Odero, the flamboyant head of the New Life Prayer Centre and Church, who was arrested on Thursday, is suspected of crimes including murder, aiding suicide, abduction, radicalization, crimes against humanity, child cruelty, fraud and money laundering.
Prosecutor Peter Kiprop said last week that there was "credible information" linking the bodies found in the forest to the deaths of several "innocent and vulnerable followers" of Odero.
Odero and Nthenge share a "history of business investments" including a television station that was used to pass "radicalised messages" to followers, Kiprop said in court documents.
The two pastors are currently in detention and are to appear in court in different towns on Tuesday.
Newly elected President William Ruto, in remarks on April 24, said there was no difference between rogue cult leader and "terrorists."
"I have instructed the agencies responsible to take up the matter and to get to the root cause and to the bottom of the activities of... people who want to use religion to advance weird, unacceptable ideology," he said.
"in the course of the week," Kindiki said, "the president (will) be announcing members of a presidential task force to deal with generally how we govern religious activities in our country and how we make sure we don't infringe on the sacred right of the freedom of worship, opinion and belief."
He added "But at the same time we don't allow criminals to misuse that right to hurt, kill, torture and starve people to death."