Boyle, who is being prosecuted after exposing unethical debt recovery practices at the Australian Taxation Office, had sought immunity under the federal public sector whistleblowing law, the Public Interest Disclosure Act.
In the South Australian District Court in March, Judge Liesl Kudelka ruled Boyle was not immune from prosecution.
In a unanimous judgment in the Court of Appeal in the SA Supreme Court on Wednesday, Justices David Lovell, Samuel Doyle and Sophie David dismissed Boyle's appeal against that decision and imposed an interim suppression order on their judgment.
The landmark judgment will determine the scope of legal protections for all Australian whistleblowers, but has been suppressed until parties have considered any parts which need to be redacted.
Rex Patrick says whistleblowers need better legal protections. (Joel Carrett/AAP PHOTOS)
Outside court, Whistleblowers Justice Fund founder Rex Patrick said the decision was "just another nail in the coffin of whistleblowing here in Australia".
"And we want people to blow the whistle when they see something going wrong," the former senator said.
"It's a critical part of our democracy, to have people on the inside reporting misconduct, and that will not occur unless we protect our whistleblowers."
Boyle is due to stand trial in the SA District Court on September 2.
Mr Patrick said there could be an appeal to the High Court if Boyle was found guilty.
"Of course, that could also happen now. Obviously, that's a matter for Richard's legal team to consider," he said.
He said Boyle was being prosecuted under laws the federal government knew were "broken".
"(Attorney-General) Mark Dreyfus has the ability, at the stroke of a pen, under Section 71 of the Judiciary Act, to drop this prosecution," Mr Patrick said.
"This is having an awful effect on Richard Boyle and his family. And it has a chilling effect on all whistleblowers or potential whistleblowers around the country."
Human Rights Law Centre senior lawyer Kieran Pender said the prosecution had demonstrated significant issues and uncertainties in Australian whistleblower protection legislation.
"Following this judgment, it is now incumbent on the Albanese government to proceed with comprehensive law reform and the establishment of a whistleblower protection authority," he said.
"Whistleblowers make Australia a better place. They should be protected, not punished."
Boyle is facing 24 charges related to the release of protected material after he claimed ATO staff had been instructed to use harsher debt collection tactics on individuals and small businesses, including orders requiring banks to hand over money, sometimes without the permission of the taxpayers.
The case includes allegations he taped private conversations without consent and took photos of taxpayer information.
Boyle first raised his concerns through internal ATO processes and then made a complaint to the tax ombudsman before taking part in a joint media investigation.
Follow-up reviews found Boyle's allegations of aggressive debt recovery practices at the ATO at the time were valid.
