Certainly the internal audit unit or the internal ethics unit should be functioning with a level of independence from line management, anyway, as part of their job. They won't ever function totally independently of the agency's interest; they still have to answer to the minister or to the head of the department. I forget your structure there or title of the head of a department.
But what is crucial is that there be a mandatory reporting relationship with the oversight agency, with the Integrity Commissioner or whoever it is.