If the leave is for two weeks, it should be applied for a minimum of 10 days in advance, and after obtaining approval from the sanctioning authority, only then should the concerned employee proceed on leave. If the employee proceeds on leave without permission, send a telegram to the address mentioned in the leave application/present/permanent addresses, which are as per his personal file, asking him to report for duty immediately. Wait for three more days and send one more telegram. After that, send a charge sheet and initiate disciplinary action—this is only one side of the coin.
As far as knowledge is concerned, no employee will proceed on leave for so many days knowing the implications. As an HR person, you should know the critical reason behind his actions. If I am not wrong, the employee might have approached the HOD with a serious cause, but the HOD might not have heard his requests and not sanctioned the leave. Sometimes, the HODs will confirm orally, and once the pressure comes from the top, they simply deny it. Please check on all these fronts. Before initiating action, look into his past record because it shall be very critical.
Regards,
Kamesh