Kenyan President Mwai Kibaki has issued an appeal for calm after the demonstrators were shot dead.
It brings the death toll during the referendum campaign to a total of nine.
The referendum is set for November 21.
The proposed constitution creates a post of prime minister but retains strong presidential powers, but has deeply divided Kenyan society and split the government.
Mr Kibaki insists the draft, the first major change to Kenya’s constitution since independence from Britain in 1963, addresses the concerns of all Kenyans.
But the political opposition, led by the son of Kenya’s founding president Jomo Kenyatta and including members of Kibaki’s coalition government, says it provides for nearly absolute presidential powers.
Dozens were injured when police opened fire on Friday during a demonstration of angry young people opposed to the planned constitution, who had gathered in the suburb of Likoni.
The demonstrators were protesting against a ban on a planned meeting of constitution critics, said police Major Simon Gatiba.
The meeting had been banned for security reasons, he said.
The rally, organised by a group of politicians opposed to the new charter, was banned because President Kibaki was in the region.
Calm returned to Mombasa on Sunday with no immediate incidents reported.
Government spokesman Alfred Mutua blamed politicians including government ministers for inciting youth to cause skirmishes.
He said police had to open fire to defend themselves after a group of youths attacked a district officer’s office.
On Saturday Mr Kibaki urged Kenyans to refrain from violence.
“We need to live peacefully irrespective of our stand on the proposed new constitution because even after the referendum we will still be together in building the nation,” he said, urging Kenyans to vote for the constitution.
But a member of his government on Saturday described the referendum as a farce.
Wangari Maathai, the 2004 Nobel peace prize winner who serves as junior environment minister, told the newspaper People’s Daily: “The referendum is a farce because it betrays the wishes of the people of
“In my opinion the debate has little to do with the text (of the constitution) and a great deal to do with power.”
Meanwhile two ministers have been threatened with treason charges for dissenting from the government line and warning that the constitution could expose the country to a coup d’etat.
Police were understood to be collecting evidence against Road Infrastructure Minister Raila Odinga and Environment Minister Kalonzo Musyoka.