There are four elements that must be present before you can consider an employee's absence to be desertion:
Once you've established that your employee has deserted, you must consider payment issues.
You MUST pay an employee who's deserted his post what's due to him
The Labour Law for Managers Loose Leaf Service explains that you still have to pay your employee any amounts due to him. This includes his monthly salary, any incentives or bonuses he would've otherwise received.
You must include things like the company loans you made to your employee before desertion in your calculation, but only if you have it in writing from your employee.
For any other amounts your employee owes you, you'd have to institute a civil claim to recover these.
You can't set these off against the amounts you owe your employee. So it'd be better for you to write off the debt from a practical point of view. The chances of recovering the money are slim considering you first have to locate your ex-employee, and then bring a civil claim against him in the Small Claims Court if the amount is under R12 000; or the Magistrates' Court.
Even if you manage to get a judgement against him there may be little or no satisfaction in enforcing execution due to your employee's lack of assets.
But the bottom line is you're obliged to pay your employee what's due to him even when he's deserted his post.
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