Joseph Buyuka was among 30 people, including self-styled pastor Paul Mackenzie of Good News International Church, in custody over the deaths of 337 followers of the church.
Jami Yamina, senior prosecution counsel, said Buyuka had died two days ago at a hospital in Malindi, about 116km from the port city of Mombasa where he had been taken from a nearby prison.
"He died ...(due to) ... complications from hunger strike and starvation, but we will await postmortem report," Yamina told a court in Mombasa.
"Two other suspects ... have also been taken ill. Police believe it is related to their hunger strike."
"The police believe that these individuals... played significant roles in the offences leading to the deaths and illegal disposal of bodies in Shakahola (forest)," court papers said of Buyuka and four others arrested with him.
Mackenzie is accused of ordering his followers to starve their children and themselves to death so they could reach heaven before the end of the world.
He handed himself over to police in April and was denied bail last month. The other suspects were arrested later after authorities started the exhumations.
He and the others have not yet been required to enter a plea.
Interior Minister Kithure Kindiki had expressed concern in May that some of Mackenzie's rescued followers were refusing food. One of them had died, he said at the time.