Hugh Flemming says he believes most doctors are honest and bill the system properly.
On Tuesday, the auditor general said some doctors have charged medicare and WorkSafeNB, which oversees workers' compensation, for the same procedures on the same patients.
Flemming said if any impropriety is found, it will be punished.
The auditor general said doctors who overcharge medicare don't face consequences, even though the Health Department has the power to revoke a doctor's billing privileges in such cases.
Flemming says he's prepared to impose sanctions or refer cases to the Justice Department or the New Brunswick Medical Society, if necessary.