STP for super purposes for subcontractor

Hi,

I’m seeking advice regarding the correct MYOB setup for one of my subcontractors and how this interacts with STP reporting and working holiday maker obligations.

The worker:
- has their own ABN,
- invoices me for completed cleaning jobs,
- works for other clients/businesses,
- can refuse work and subcontract work if desired,
- supplies their own transport and insurance,
- and is treated as an independent contractor under our agreement.

However, as they are paid mainly for labour, I have been paying superannuation for them as a contractor deemed “employee for super purposes”.

To process their super through MYOB, I currently:
- have them set up in payroll,
- run a $0 pay run weekly,
- enter only the super amount,
- and lodge through STP so the super can then be processed.

I do not process wages or PAYG withholding for them.

The worker is on a Working Holiday Visa, and I have now received an ATO notice stating that:
- the worker did not declare they were a working holiday maker,
- and that I may need to withhold tax using the working holiday maker tax table.

My concern is that the STP/payroll setup may be causing the ATO to treat the contractor as an employee for PAYG purposes, even though they are only in payroll to facilitate superannuation processing.

Could you please advise:
1. Whether my current MYOB setup is the correct way to handle a contractor who is only an employee for super purposes;
2. Whether there is a cleaner way to process super for this type of contractor without triggering employee/WHM payroll reporting;
3. Whether changes should be made to the employee card, TFN settings, PAYG items, or STP setup;
4. Whether historical STP reporting should be amended or left as-is.

I want to ensure the setup is fully compliant while still correctly reflecting the contractor relationship.

Thank you for your assistance.