Okay, companies can't declare themselves bankrupt - bankruptcy doesn't apply to companies, only people.
What your company is likely to be is insolvent. There's no problem with this as long as you don't breach the Corporations Act, such as by trading while insolvent. For example, incurring further debts without a reasonable expectation that you will be able to pay them.
Your options are, realistically, find an injection of capital to pay the debt (bearing in mind the above warning that you only do so if you have prospects of trading to pay the loan back), appoint a liquidator to wind the company up (which will cost money the company doesn't currently have - again a 'no no'), or do nothing and allow the company to be eventually wound up by the ATO if the debt is significant enough. That way, the liquidator is appointed by the court and the company doesn't have to pay for it.