Ghislain Picard says an investigation into the allegations, including those detailed last week on Radio-Canada's investigative program Enquête, should not be led by another police force.
"If there are other cases of abuse by the force the fear is that the victims aren't going to come out and make a complaint," Picard told CBC Montreal's Daybreak.
Several women are accusing Quebec provincial police officers of sexual assault and abuse of power. Eight officers have either been put on leave or transferred to administrative duty following the allegations.
The investigation, which was launched last May, was transferred last week from the Sûreté du Québec to Montreal police.
Picard also said the allegations raise questions about the relationship between police and aboriginal people across the province.
Not an 'easy relationship'
Provincial opposition parties have also called for an independent inquiry.
The Quebec government says it should be done as part of a countrywide inquiry into missing and murdered aboriginal women, which was promised by prime minister-designate Justin Trudeau.
"Anything we do in Quebec has to be complimentary to what the federal government is going to do," Quebec's Aboriginal Affairs Minister Geoff Kelley told Daybreak.
Kelley said the Montreal police force was brought in to provide "reassurance" to the population the investigation would be conducted fairly, adding that First Nations and police have historically not had "an easy relationship."
"We have to sit down and restore confidence in our police forces, because that's what we need in our society," he said.
He added that the Quebec government plans to set up an independent body by early next year that will be able to investigate allegations against police.
After meeting with local leaders and residents on the weekend, Kelley said the province needs to find ways to improve the situation there quickly.
The chiefs of Quebec's First Nations will meet in Val-d'Or tomorrow.