I don't think that a manager should audit his own dept. as a function of the "official" formal internal audit. Obviously he should be performing audit functions on a daily basis. He must know how his dept / process is operating! But for internal audit purposes, a separate and objective view is what is called for. This is the checks and balances system.
From where I sit, if he is the process owner, department manager, whatever you want to call him, ..if he has reporting responsibilities and accountability for the functioning of that process, dept, whatever,..then it is someone else who must be doing the auditing.
It comes down to "who is responsible/accountable for the successful functioning of this process?" and "who will be responsible for taking corrective action should any be needed based on the audit findings?". If the manager is either of these people, he does not belong in the internal audit role.