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First and foremost it is important to have a defined employee ID or number sequence which should be embedded on the personnel file for ease of arrangement. Secondly, you should have an approved checklist of documents which are mandatory and file the documents collected from the new joinee and tick against the respective check box. This allows for control and followup on missing documents by creating a excel tracker. The responsibility of completing the employee file can be rested on the identified resource by tracking this excel on a specified frequency.
In HR it is recommended to use forms wherever possible and control them using unique form numbers and track each form using sequence numbering. All documents to be filed based on staff code. These are few of the very general and obivious best practices for HR personnel files.