In an interview with The Canadian Press, Kathleen Wynne says it's "outrageous" for Harper to say that there's not a systemic aspect to the troubling issue.
All the provinces and territories have endorsed calls for a national inquiry, which the federal Conservatives have rejected.
The death of a 15-year-old aboriginal girl found wrapped in a bag and dumped in the Red River has prompted renewed calls for an inquiry.
Tina Fontaine, whose body was discovered Sunday, had been in Winnipeg less than a month when she ran away from foster care.
But Harper says most such cases are addressed and solved by the police, adding it's important to keep in mind that these are crimes.