Kenya police on Tuesday announced a manhunt of two key leaders behind an upsurge of radicalization in the tourism resort city of Mombasa.

County CID commander Henry Ondiek said they are looking for the two suspects who escaped police dragnet when they raided Masjid Mosque on Sunday.

"Two aliases Rambo and Ramadan are key Al-Shabaab members behind recruitment and funding of Al-Shabaab activities in the country," Ondiek told Xinhua in Mombasa. "We believe they escaped with injuries when the police raided the mosque," he added.

The CID commander said intelligence report indicates that the two are Al-Shabaab returnees. They had undergone various military training in Somalia before returning to plan more attacks.

Kenyan police have engaged stone-throwing Muslim youth in streets of the coastal city in the past two days after two people were killed and dozens injured in the similar chaos on Sunday.

The confrontation between police who were armed with rubber bullets and the youth forced several businesses near the Masjid Msa Mosque to shut down as roads were blocked and cars smashed in the tourism resort city.

On Tuesday, Muslim clerics announced that the two Mosques Sakina and Masjid Musa Majengo are now under the control of radical Muslim youths. The Council of Imam and Preachers of Kenya CIPK leadership said the youths took over the mosques after they managed to oust the committee members.

CIPK chairman Sheikh Mohammed Idris termed the Sunday meeting at Sakina Mosque as Jihad convention.

"We are aware the radical youths had converged for jihad meeting with bad intention for the country," Idris said. The cleric urged the police to deal decisively with radicalized Muslim youths causing violence in the name of Islam in Mombasa.

The cleric claims the youths have taken over the Mosques with fears that more youths will be radicalized if the government does not take swift action.

The leaders opposed the alleged "Jihad teaching" saying they are being misinterpreted by the youths.

Idris urged the government to arrest the key financiers and radical preachers using innocent youths for their own interest, saying Islam religion is peaceful and does not propagate for violence.

The government on Tuesday said it was considering shutting down two mosques in Mombasa following Sunday's clash between Muslim youth and police. The leaders however oppose the decision.

Some 129 radical youths arrested on Sunday were arraigned in court on Monday, when they were charged with being connected to the Al-Shabaab terrorist group. But they were not allowed to take plea.

Senior Resident Magistrate James Wambura ordered the suspects remain in remand at the for five days to allow the prosecution to complete investigations into the allegations.

Mombasa, the country's second largest city and a major tourist spot, is one of various cities targeted by a series of grenade attacks and abduction of foreigners in recent months.

Police sources indicate that the Al-Shabaab recruits are planning to carry out revenge attacks in the country.