Unfortunately the solution to this problem is lengthy. You will need to go into a SARS office and sit with a consultant who will then ask you to complete a sworn document stating that your employer didn't pay over your tax nor provide you with a salary slip. You should take your bank statements showing the amount coming into your account each month. I would also take with your employment contract if you have one to prove your income.
Are you 100% sure your employees tax wasn't paid over? If that is the case then SARS will expect you to pay over the tax owed. Your employer will be fined for this and have to pay severe penalties. You must get SARS to check this for you. Hopefully your employer has paid over the employees tax and just didn't record it correctly. They will be able to tell you this.
If you do have to pay over the tax and don't have that amount of cash available, SARS are open to making payment arrangements. Ask them to wavier the penalties and interest as it was not your fault. The should be open to this.
I hope this helps, please feel free to ask any more questions if you need anything else.
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