What will an Internal Auditor who discover flaws in the records of one department in his Company do?

Internal Auditor usually have to report at the higher level like Director, Audit Committee etc. Internal Auditor should carry on investigations from the manager of that department. He should further analyze that either it is a weakness in the internal control procedures or human error or intentional manipulation. Intentional manipulation is dangrous and must be investigated in detail.

Write about the disparities, and discuss with the departmental head, get the corrected. If it fails report to the Audit committe which will enforce correction.

Before reporting to high authorities he should brief his manager about the situation and if agreed evidence should be collected first. An analyze should be done to identify whether it is a weakness is internal control or a deliberate intrusion following with a recommendation to relevant authorities.

the report of the auditing must be reviewed , making quick analysis , making detailed analysis then taking a corrective action

including his reporting he must be refer to this point and aslo must be submit his opinion to slove this point  

If any such practice has been observed then violation or non-implementation of departmental procedure must bring into notice of concern head and QMS department alongwith CC to top management. Chances exist that this malpractice will affect the certification of the organization and detail or explanation to be taken from concern head(s) in case of non-conformity.