Kenyan authorities say the dead were members of the Good News International Church led by self-proclaimed pastor Paul Nthenge Mackenzie, 50, who had predicted the world would end on April 15 and ordered his followers to kill themselves to be the first to go to heaven and "to meet Jesus."
The death toll stands at a total of 109 so far, with 101, mostly children, found in mass graves and eight people found alive who later died - but could rise further.
The small courtroom in Malindi was packed with relatives of victims as Mackenzie was brought in by about half a dozen police officers along with eight other defendants.
After a brief hearing, the case was moved to the high court in Kenya's second-largest city of Mombasa, where the suspects will face terrorism charges, prosecutor Vivian Kambaga told AFP.
"There is a court (in Mombasa) that is gazetted to handle cases under the prevention of terrorism act," Kambaga told a magistrate during the hearing in Malindi, asking for the case to be moved to the high court.
Ezekiel Odero, a wealthy and high-profile televangelist, is also expected at the high court in Mombasa following his arrest in Malindi on Thursday in connection with the same case.
The first autopsies from Shakahola were carried out Monday on nine children and one woman.
They confirmed starvation as the cause of death, though some victims were asphyxiated, the authorities said.
Odero is suspected of murder, aiding suicide, abduction, radicalisation, crimes against humanity, child cruelty, fraud and money laundering.
The prosecution is seeking to detain him for a further 30 days, citing credible information linking the corpses exhumed at Shakahola to the deaths of several "innocent and vulnerable followers" from Odero's New Life Prayer Centre and Church.
Cliff Ombeta, one of Odero's lawyers, told reporters upon arrival at the court that there was no evidence connecting the pastor to the Shakahola discoveries.
"Evidence must be brought. It is a case where you must prove," he said.
A crowd of Odero's supporters gathered outside the court, singing and praying, while some were in tears.
In addition to the terrorism charges prosecutors plan to file, Mackenzie stands accused of murder, kidnapping, cruelty towards children among other crimes in court documents seen by AFP.
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 have linked Odero and Mackenzie, saying in court documents that they share a "history of business investments" including a television station used to pass "radicalized messages" to followers.
In his filing to the court, Odero said he wanted to "strongly disassociate" himself from Mackenzie and disagreed with his teachings.
The horrific saga has seen President William Ruto vow to intervene in Kenya's homegrown religious movements, and thrown a spotlight on failed efforts to regulate unscrupulous churches and cults that have dabbled in criminality.
This week Ruto will set up a task force on how to govern religious activities in Kenya, home to about 4,000 churches, Interior Minister Kithure Kindiki said Monday.
He said the government must "make sure we don't infringe on the sacred right of the freedom of worship, opinion and belief - But at the same time we don't allow criminals to misuse that right to hurt, kill, torture and starve people to death."
This report was sourced from Agence France-Presse and Reuters.