I have recently noticed a new deduction of 5% of my billings for company payroll tax. There is nothing mentioned in NTCER about this but my Practice Manager advised that this is an allowable deduction. Is this correct?

The NTCER outlines your minimum employment terms and conditions

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Payroll tax is a business expense and should NOT be deducted from employee wages. So as GP registrars, employed according to the NTCER are considered to be employees, payroll tax should not be deducted from the percentage of your billings. The percentage of your MBS earnings that are retained by the practice (e.g. the practice retains 50.73% of your billings, if you are paid according to NTCER minimum) is to cover business costs including payroll tax.