Sympathisers of the Somali Islamist rebel group al-Shabaab took part in Friday's protest to demand the release of a detained foreign preacher that left one dead.
Internal Security minister George Saitoti said Saturday that the demonstration was infiltrated by "foreign youths waving placards with extremist ideas."
Some protesters carried the black flag of the hardline Somali rebels, a group accused by the US of links to al Qaeda. The militia is also trying to overthrow the fragile Somalia Government and impose its own harsh version of sharia law.
"Intelligence reports indicate that these individuals are sympathetic to al-Shabaab," said Prof Saitoti.
He added that radical Jamaican Muslim preacher Sheikh Abdullah al-Faisal, who is on an international terror watch list, will be deported "without any delay."
"The government will not entertain illegal aliens or foreigners with criminal intentions into the country."
Prof Saitoti said that police cancelled the demonstration after intelligence showed it would turn violent.
"Intelligence information received indicated that the demonstration would be infiltrated by violent foreign elements from a neighbouring country including criminals out to cause mayhem."
He assured Muslims of continued protection of their rights adding that the foreign elements wished to portray that the government was unfairly targeting the community.
"I wish to assure all Muslims and other law abiding citizens that the government is committed to the protection of religious freedom and civil liberties," he said.
The minister defended the police saying that they exercised restraint in the face of provocation from rowdy youths.
"The police did everything possible to contain the situation within the rules of engagement despite the highly provocative act of physical attacks," said the Internal Security minister.
He said that in the fracas, two people "Abdallah Kola and Mohammed Noor were injured on the leg near the ankle and forehead respectively."
The minister said one security officer was hit by a bullet believed to have been fired by a demonstrator.
Prof Saitoti also announced that an inquiry to investigate the matter will be formed.
At the same time, Prime Minister Raila Odinga has appealed to the Muslim community to remain calm and give the government time on their grievances.
He said: "The confinement of the cleric is a sensitive security matter that the government is handling delicately and it should be given time."
Mr Odinga also urged the police to refrain using live rounds to contain riots.
Mr al-Faisal arrived in Kenya on December, 24 last year after travelling through Nigeria, Angola, Mozambique, Swaziland and Malawi and Tanzania.
He had been deported to The Gambia last week on the orders of Immigration minister Otieno Kajwang, but was returned on Sunday morning after Nigeria refused to give him passage.
Additional reporting by PMPS