The ATO conducts audits where they consider a more in-depth examination of the issue is required. The ATO seeks your cooperation so they can complete audits as quickly as possible and give you certainty of your tax and super position.
The ATO will provide you with a clear escalation point to resolve issues with them. You will be provided with the contact details of an executive level officer in the Audit management plan. You should contact this officer if your assigned officer does not meet your expectations or you have any other concern.
More information, including what the typical audit process entails, can be found here.