After furious street battles yesterday in which four protestors died -- three from stab wounds and one shot -- and a church was torched, the city was largely quiet overnight and remained so today, police said.
"I have just been around to monitor the situation... And can report that calm has returned everywhere," said regional police chief Robert Kitur.
Yesterday, protesters hurled stones and armed paramilitary police fired tear gas near a mosque, some of whose leaders have been accused of links to Somalia's Islamist Shebab, insurgents who massacred 67 people in Nairobi's Westgate shopping mall last month.
The assassination mirrored the murder of another extremist cleric last year that provoked days of deadly riots.
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Slain cleric Sheikh Ibrahim Ismail was viewed as the successor to Aboud Rogo Mohammed, a controversial preacher on US and UN sanctions lists for allegedly supporting the Shebab, who was shot dead in August 2012.
Mombasa is Kenya's main port and a major tourist hub, popular with visitors coming to enjoy the white sand beaches on the Indian Ocean coastline.
Like in the case of Rogo, radical preachers have said the killing of Ismail was an "execution" by the police, which denied the claim.
"We are not involved in anyway with the killings," Kitur said. "Anyone with evidence of police involvement in that killing should come and see me in person."
The killing of Ismail follows attacks last month by the Al-Qaeda-linked Shebab, who launched a deadly assault on an upmarket Nairobi shopping mall in a four-day bloodbath.
Meanwhile foreign special forces staged a nighttime sea and air attack on a key Shebab base in southern Somalia, the insurgents said today, claiming the assault had failed.