The deaths occurred when police tried to re-establish control in the La Saline slum, a bastion of pro-Aristide militias.
The incident comes less than 24 hours after Prime Minister Yvon Neptune declared a state of emergency in the country.
A close ally of former president Jean-Bertrand Aristide, Neptune has remained in office and continues to condemn several illegal groups "fomenting terror in the capital".
The veiled reference was to the rebels patrolling Port-au-Prince after making a triumphant entrance into the capital after Aristide left the country on Sunday.
Although insurgents led by Guy Philippe had agreed to disarm, deadly gun battles between rebels, police and gangs loyal to ex-president Jean Bertrand Aristide continue.
Beefing up security
However, US Marines and French forces have begun patrolling the streets in light armoured vehicles to limit the resurgence of killing, looting and arson that erupted in recent days.
French and US troops plan to
increase the number of patrols
Philippe has also met with the international force commander, US Marine Colonel Mark Gurganus, to discuss security guarantees and disarmament.
It was the first meeting between the two sides since the uprising began last month.
On Monday, emboldened by his rapturous welcome on entering the capital, Philippe said he was in control of the country and that his troops would not lay down their weapons until the pro-Aristide gangs, or "chimeres," were also disarmed.
The rebels had also threatened to arrest Prime Minister Yvon Neptune although the US Marines are protecting what remains of the legitimate government.
Five days after his arrival in the Central African Republic, former president Jean-Bertrand Aristide has been placed under what amounts to a house arrest.
According to Aristide's lawyer, Ira Kurzban, the Republic has prevented the former premier from making or receiving international phone calls.
Kurzban also claims that French soldiers are guarding the president in a building he is not permitted to leave.