The Fair Work Commission has found Mr Shamir's sacking was harsh, unfair, unreasonable and indefensible. But the ATO will not accept the verdict and had a legal win on Friday with the full bench of the commission quashing the original decision and agreeing to hear the case again. Mr Shamir presented a dossier of evidence last year to the taxation watchdog, the Inspector-General of Taxation, supporting allegations that the ATO broke the law with its "covert operations" against an unknown number of innocent taxpayers. Much of what is alleged cannot be disclosed by Mr Shamir under the strict secrecy provisions the ATO imposes on its current and former employees and Inspector-General Ali Noroozi said he could not discuss the case. But documents, released by the ATO under freedom of information, reveal that Mr Shamir warned his bosses in 2012 they were engaged in an overzealous response to a court decision that reined in the ATO powers to withhold tax refunds.

The revenue agency stands accused of secretly cancelling large numbers of tax refunds without informing the taxpayer or giving them the right of objection, using the misleading and unproven justification that "ID takeover" had occurred by an "unknown third party". The ATO more than doubled the amount of money it withheld in the year it began its secret operation and scored more than $56 million the following year in extra government funding to tackle ID fraud. But according to the complaints by Mr Shamir, revealed by the FOI documents, many of those cases may have been trumped up with the Tax Office using a crude, "guilt by association" approach to declare fraud against taxpayers with little or no evidence. The Tax Office said in a statement on Friday that no innocent taxpayers had been caught up in its anti-fraud operation and cited "privacy" in saying it would not discuss its dispute with Mr Shamir. Soon after taking his concerns to the Inspector-General in 2015, Mr Shamir was sacked over "non-performance of duties".

But he had an initial win in April when the Fair Work Commission described it as unfair, harsh, unreasonable, indefensible with "too many holes in the ATO's case". Mr Shamir believes he was removed from the Tax Office to stop him from co-operating with the investigation into the ATO's "Operation Whip" and other covert programs put in place in 2011 after it lost a court battle over its anti-fraud programs. After Friday's setback Mr Shamir, who is now awaiting a new decision from Fair Work on whether he will be re-instated, told Fairfax that all he ever wanted was to do his job. "From the beginning of the dispute in mid-2013, all I've wanted is to be able to go back to work," he said. Mr Shamir said he had made his whistleblower disclosure and was happy to leave the case with the Inspector-General and get on with his career.

"The ATO say that there is a loss of trust in the relationship because I have made disclosures about the ATO," the former tax official told Fairfax. "However, my view is that I have put those matters in the hands of authorities. "They are no longer my direct concern, other than to assist authorities if requested, and that is not a reason I should not return to work at the ATO. Loading "I did my job diligently, including to ensure Australians can have confidence in their Tax Office.