What you need to know:
- Ten were bundled into a police van at Majengo area while two others were taken into custody near Msikiti Musa in the restive town.
- Somalia militia Al-Shabaab called on Kenyan Muslims to "take all necessary measures" to protect their religion.
Twelve people have been arrested in Mombasa during a confrontation between police and rowdy youth protesting the killing of radical cleric Aboud Rogo.
Ten were bundled into a police van at Majengo area while two others were taken into custody near Msikiti Musa in the restive town.
Earlier, tension was high as the protests entered a second day.
Police lobbed teargas at the protestors a during the morning standoff.
In Majengo, the officers fired rubber bullets to disperse the marauding demonstrators.
One person was stabbed as the mayhem reigned.
Sylvester Odhiambo, a mechanic, received first aid at the Salvation Army Mombasa Central Church.
As the riots raged, Somalia militia Al-Shabaab called on Kenyan Muslims to "take all necessary measures" to protect their religion.
"Muslims must take the matter into their own hands, stand united against the kuffar (unbelievers) and take all necessary measures to protect their religion, their honour, their property and their lives from the enemies of Islam," the Shabaab said in a statement.
Prime Minister Raila Odinga has condemned the killing of Sheikh Aboud Rogo.
Mr Odinga said the killing was an act of thugs and should not ignite violence between Christians and Muslims.
The PM directed Police Commissioner Mathew Iteere to ensure the killers were arrested and charged in court.
"The killing is a most heinous act. On behalf of the government, I condemn the killing. Assassination is not acceptable by the government. We will not accept wanton killing of innocent Kenyans. Even if one is suspected of a crime, the law should be followed. We cannot run the country by rule of the jungle,” Mr Odinga said.
Speaking to journalists at his office in Nairobi, Mr Odinga called for calm as the government pursues the killers.
"We don’t want inter-religious war to erupt out of this as the killing has nothing to do with religion. Just like I did in Garissa where a church was attacked recently, we appeal to Muslims not to link religion into this. Lets control ourselves as Kenyans,” Mr Odinga said.
"Let's act with restraint as law enforcement agencies get to the root of the matter. We urge Muslims and Christians not to fight,” Mr Odinga said.
At the same tine, Planning assistant minister Peter Kenneth condemned the Mombasa riots and urged restraint.
"I appeal to our brothers and sisters in Mombasa to exercise restraint, shun violence and aim for peaceful coexistence for all our people," he said on Twitter.
On Monday night, hours after Sheikh Rogo was shot dead by unknown gunmen, protesting youth looted businesses and burnt tyres.
Four churches were also attacked in Mombasa.
The fiery madrassa teacher, named by the United Nations and the US as Al-Shabaab’s chief agent in Kenya, was shot near Bamburi on the Mombasa-Malindi highway as he drove his wife to hospital.