The obvious answer is you haven't paid enough tax. Perhaps your employer isn't withholding quite enough tax from your pay?
If that turns out to be the answer, and your total owed is around $1k, I wouldn't personally correct that with my employer. I'd prefer to have the use of that $1k throughout the year and pay the ATO what I owed at the end.
Just to note, you can set up a repayment plan fairly easily. Just call up the ATO and state how much your comfortable with paying back, divide it up to end roughly same time next year. Minimises the bill shock.
If you have a HECS debt, it may be due to the fresh increase to indexation
Indexation doesn't affect how much HECS you owe per year though, only the lifetime total balance.