Const. Chantal Farrah says the officer was shot early Wednesday morning in the Campbellton area while on duty.
"We have requested that the Surete du Quebec conduct an investigation into what happened," she said, while refusing to explain why the outside force had been called in.
The incident occurred in the small community of Flatland on the outskirts of Campbellton, which is on the province's north shore.
Sgt. Ann Mathieu of the Surete du Quebec, that province's police force, said 10 officers have begun interviewing potential witnesses, the injured officer and another officer who was with him.
"We are investigating the circumstances regarding this event," she said.
She would only say that there were two officers involved and that the man who was shot did not sustain life-threatening injuries.
"We are verifying the type of intervention they were doing. We are verifying if it was a call that they received. It is the kind of questions that we are checking at this moment," she said.
While Mathieu said investigators are still trying to determine the circumstances, they believe it was an isolated incident and there is no danger to the public.
Police have not released the injured officer's name.