Detectives from FBI and Scotland Yard on Tuesday shut down a suspected terror cell in Likoni, Mombasa.
It has been registered as a madrassa and a rehabilitation center.
Two Islamic preachers from the Al Madrasatul Falan cell were arrested in the covert operation and more than 90 children were taken to police custody.
The children are from as young as five and said to be from different countries including US, UK, Canada, South Africa, Saudia Arabia, Somalia, Zambia, Uganda and Kenya.
They are being questioned at the Coast Regional Police Headquarters.
Officers are seeking to establish who their parents are, whether they have been undergoing indoctrination and if they have undergone physical or sexual abuse.
The religious leaders were handed over to the officers from Anti-Terrorism Unit and Director Criminal Investigation for interrogation.
A senior officer leading the operation told The Star that the UK government is interested in one captive, a Syria returnee from UK, traced to the Madrasa.
Detectives say the 20-year-old has valid travel documents and was sent to the center by his parents. He is alleged to be an IS member.
“He was sent to the country as part of the punishment,” the officer who sought anonymity said.
