Write to the ATO laying out all the facts, and ask them to register it as a complaint. Insist on a formal written reply.
Frankly I have to wonder where your accounts office is in all of this as they should be dealing with the ATO, and should know their way around.
Maybe ask the accounts office for documentary proof of what they claim, as ask them why you are in such a situation. And if the accounts office does not know then maybe some new staff?
