I have managed to negotiate a percentage of 50% billings, but my practice is taking super out of that percentage. Is this allowed?

The NTCER outlines your minimum employment terms and conditions

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It depends on what is stated in your employment agreement.

If your employment agreement states that the percentage of gross billings is “50% inclusive of superannuation” then, as the superannuation rate is currently 11.5%, your salary is actually 44.25% of billings with 5.75% billings paid into your superannuation fund. (This is below the NTCER minimum, which is 44.79% billings as salary and 5.15% billings is the super contribution, total 49.94%)

However, if your agreement states that the percentage of gross billings is “50% plus superannuation” or “50% exclusive of superannuation”, then the superannuation contribution should not be deducted from your 50% billings rather 5.75% (i.e. 11.5% of 50%) of your total billings is paid into your superannuation fund on top of the 50% of your billings which forms your salary.