The centre in Likoni was registered as a Madrassa and rehab facility.
According to The Star, the raid netted over 90 children suspected to be trafficking victims. The building was suspected to be a terror cell.
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 as young as five and said to be from different countries including the US, the UK, Canada, South Africa, Saudia Arabia, Somalia, Zambia, Uganda and Kenya and are being held for questioning at the Coastal Police HQ.
Officers are trying to determine who their parents are, whether they have been undergoing induction and if they have undergone physical or sexual abuse.
The preachers were handed over to the Anti-Terrorism Unit and Director Criminal Investigation for interrogation.
The officer in charge of anti Human Trafficking and Child Protection Unit in the DCIO, Grace Ndirangu, said they raided cell following cases of mistreatment of kids.
A similar raid was conducted in Isiolo recently.