Police said the profiling of terror suspects found some of them had attended the Machakos madrassa
The authorities in Kenya say they have closed a madrassa near the capital for teaching radical Islamic ideologies.
The religious school in Machakos, about 65km (40 miles) east of Nairobi, was targeted after some youths in the area were detained on suspicion of being recruited to join Somali militants.
The police’s Criminal Investigation Department (CID) chief has warned that other radical madrassas will be shut.
Somalia’s al-Shabab group has carried out a spate of attacks in Kenya.
The al-Qaeda affiliate says they are in revenge for the presence of Kenyan troops in Somalia and the killing of Muslims.
A year ago, 67 people were killed when the group’s fighters laid siege to the upmarket Westgate shopping centre in Nairobi.
The BBC’s Abdullahi Abi in Nairobi says it is the first Kenyan madrassa to be shut down by the police because of its extremist teachings.
Interior Ministry spokesman Mwenda Njoka told the BBC the decision was taken to close the Daarul-Irashad centre, which opened in 1997, on the advice of the police’s CID, anti-terror and intelligence units.
The recent arrest in the Machakos area of 21 young men suspected of being recruited for al-Shabab first raised suspicions, he said.
The police then profiled suspects arrested in other terror crackdowns and found that others had passed through that madrassa, the spokesman said.
Machakos is a large town with a minority Muslim population that has not been subject to any attacks.