What are the threats or risks to the organization due to having an Internal Auditor? I mean, what problems can internal auditors bring?

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Believe it or not, internal auditors can cause trouble. Anything that designed to bring benefit, can cause problem if misapplied. From experience, the problems that were absent in the absence of Internal Audit and have emerged due to having Internal Audit(or)units, are mainly:

A) Fear in employees due to the feeling that they will be punished for their minor deficiencies. This is a misconception. However, it affects employee morale and psychology, thus performance.

B) Internal auditors may recommend something wrong with the believe that it will fix the current deficiency.

C) Management will be relaxed and will have a loose attention and weakly disciplined self-check environment for matters related to risk, control and fraud because of too much reliance on internal auditors. Oftentimes, managers think that internal auditors will highlight all their problems.
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