It prompted a joint investigation by The Age, The Sydney Morning Herald and ABC that triggered legal action from Tax Office Commissioner Chris Jordan.
Under a deal reached with the Nick Xenophon Team in 2014 for its support for the union-busting Registered Organisations Commission, the Coalition promised it would push through whistleblowing protections for private and public organisations.
The measures for private corporations passed in the last sitting weeks of Parliament but, with only two Senate sitting days left, the government has run out of time to get the laws through to apply the same protections to public servants.
«They haven’t progressed it fast enough,» said Centre Alliance senator Rex Patrick, from the party formerly known as NXT.
«I think the ATO needs to act in accordance with the philosophy accepted by the government that whistleblowers need to be protected. Mr Jordan appears to have taken a different view.»
Mr Boyle has previously said he made a 12,000 word disclosure to the Tax Office, but claims this was rejected by tax authorities. The Australian Federal Police raided his home days before he went public and only a month after the ATO offered him a settlement to prevent him from speaking out.
A.J. Brown, a member of the federal government’s expert whistleblower panel, said that disclosure could give Mr Boyle protections under Public Interest Disclosure Act.
«If he did do that it wouldn’t matter that they rejected it. On the face of it the subsequent action would vindicate him,» Professor Brown said.
In the wake of the revelations, a bipartisan House Standing Committee on Tax and Revenue recommended a new Tax Office charter, an appeals group headed by a second independent commissioner, the transfer of debt-recovery functions into the ATO’s compliance operations and a restructure of compensation processes.
The Griffith University professor said if Mr Boyle’s initial disclosure was proved, it would be a conclusive defence and Mr Boyle might be able to claim compensation.
«It would wipe out the charges at least,» Professor Brown said.
He described the ATO’s decision as a normal knee-jerk reaction from any organisation seeking to discipline its employees to maintain professional confidentiality.
«Agencies go on leak hunts, sometimes those are justified, sometimes they aren’t,» he said. «This appears to be a case where they should be thinking about the spirit as well as the letter of the Public Interest Disclosure Act.»
Ken Phillips, the executive director of Independent Contractors of Australia, said the ATO’s pursuit of Mr Boyle was another attempt to «cook him slowly».
«Certainly in our view, the behaviour of the ATO towards Richard is very much an attempt to send a signal: ‘We are doing to Richard what we can do to you if you are whistleblower’.»
Labor has pledged to bring existing private and public whistleblowing laws under a single Whistleblowing Act and establish a Whistleblower Protection Authority with a rewards scheme.
A spokesman for Assistant Treasurer Stuart Robert said he was not able to comment as the matter was before the courts.
An ATO spokesman said the Tax Office could not comment on prosecution decisions made by the Commonwealth Director of Public Prosecutions.
«We note the charges relating to Mr Boyle concern the alleged disclosure of confidential taxpayer information, recording and disclosing tax file numbers, and the use of listening devices,» he said.
with Adele Ferguson
Eryk Bagshaw is an economics correspondent for The Sydney Morning Herald and The Age.