"This is an astonishing use of public resources, to investigate someone who has passionately and with every fibre of my being tried to assist taxpayers in meeting their tax obligations and to enforce taxpayers who are ripping the country off by not paying their fair share of tax," he said.
Mr Boyle said the officers arrived at his door about 8:00am.
He was still in his dressing gown and didn't have time to change.
He attempted to film the raid but the AFP officers seized his mobile phone, and the phone of his fiancee.
"They've spent the past couple of hours going through our drawers, going through our personal belongings and documents," he said.
The intervention by officers from the AFP and the ATO comes as the Four Corners program prepares to air its investigation into the extraordinary powers of the ATO.
The warrant specifically refers to Four Corners and Fairfax reporter Adele Ferguson, and alleges that Richard Boyle had illegally taken either originals or copies of taxpayer information, photos of ATO computer screens or emails.
Mr Boyle said there was some suggestion from the AFP and ATO officers at his home that he had committed a crime in speaking to the media.
"It's absolutely astonishing. I'm horrified that this organisation has these powers over the community and I think things need to change," he said.
Mr Boyle has had a series of previous run-ins with the ATO.
In 2016 he was formally reprimanded and had his salary docked, for accessing client records against ATO policy and against advice and cancelling interest charges imposed on taxpayers without ATO approval.
Mr Boyle told Four Corners and Fairfax he was only ever trying to assist those taxpayers.
He was suspended with pay last September over another alleged breach of the Public Service Code of Conduct.
The ATO tried to settle with him in February, offering him a payout and a statement of service, with no admission of liability.
He decided to knock it back to speak to Four Corners and Fairfax.
The Tax Office has since suspended him without pay and his future with the ATO still hangs in the balance.
In a statement, the ATO said protecting confidentiality was "critical for the integrity of Australia's tax and super systems".
"Today, swift action was taken, in the execution of a search warrant against an individual in Adelaide, to secure information which we believe was obtained contrary to our secrecy obligations," the statement said.
"The Commissioner is committed to doing everything possible to secure taxpayer information, and will pursue cases where taxpayer confidentiality has been compromised."
The ATO said there was an ongoing investigation with the AFP.
Four Corners and Fairfax reporter, Adele Ferguson's investigation into allegations of abuse of power by the ATO is due to air on Four Corners next Monday. (9th April 2018)