I get paid the base rate fortnightly as per the NTCER. At the end of the billing cycle my percentage of my total billings is calculated and the difference between this and the base rate, that has already been paid to me over the cycle period, is my bonus.
I took some leave during the recent billing cycle and, as a result, the base rate pay that I received over the cycle was actually a bit more than my percentage calculated on my total billings for this cycle. Does this mean I have to pay back the difference as my percentage of billings is less than the base rate payment made for this billings cycle?

The NTCER outlines your minimum employment terms and conditions

Read the full NTCER

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The NTCER (Schedule A) states that registrars are to be paid the higher of:
(a) base rate of pay or

(b) percentage of billings calculated over the cycle (which is a monthly interval in this case).

This essentially means that registrars are guaranteed to receive, as minimum remuneration, the base rate of pay. If your percentage of billings is less than the base rate paid over a cycle, then the base rate is the only remuneration you will receive for the cycle interval; furthermore, you do not have to pay back any difference.