The bodies in the new case are believed to be buried in shallow graves on the outskirts of Malindi in southeastern Kenya's Kilifi County, and 11 suspects are being investigated, Kenya's Office of the Director of Public Prosecutions said on X.
"Investigators suspect multiple individuals were murdered through starvation and suffocation," it said.
"The victims may have been starved and suffocated as a result of adopting and promoting extreme religious ideologies."
More than 400 bodies were exhumed from the nearby Shakahola Forest in 2023 in one of the world's worst cult-related disasters in recent history.
In that case, prosecutors have alleged that cult leader Paul Mackenzie ordered his followers to starve themselves and their children to death so that they could go to heaven before the world ended.
Mackenzie, who faces charges of murder and terrorism, denies the accusations against him.
The prosecutor's office said people in the area of the recently-discovered graves had been unable to account for the whereabouts of several children, leading to suspicion of foul play.
The court ordered the exhumations to be followed by post-mortem examinations, DNA testing and toxicological analysis, it said.
In April, Kenyan police also recovered two bodies and rescued 57 people who looked weak and frail from a church in the country's west.
