Tax Commissioner Chris Jordan has taken the extraordinary step of talking in detail about the affairs of individuals while before Parliament.

Key points: ATO boss Chris Jordan has taken issue with claims made in the media's Right to Know campaign

ATO boss Chris Jordan has taken issue with claims made in the media's Right to Know campaign He told Senate Estimates the ATO takes whistleblowing very seriously

He told Senate Estimates the ATO takes whistleblowing very seriously He said the ATO terminated two former employees, Richard Boyle and Ron Shamir, for reasons other than blowing the whistle

At Senate Estimates on Wednesday Mr Jordan used parliamentary privilege to hit back at what he labelled "sensational" media reporting about the way Australian Taxation Office (ATO) whistleblowers Richard Boyle and Ron Shamir had been treated after making allegations of misconduct about the ATO.

He said both former employees had been the subject of "ongoing workplace performance or conduct issues that were close to finalisation and likely to result in their termination", and they were not sacked because of their whistleblowing activities.

Mr Jordan said the public "Right to Know" campaign that kicked off on Monday highlighting restrictions on media freedom had "reignited misleading public commentary about the tax office's attitude towards whistleblowers".

He said the accompanying reports and editorials, including those from the ABC, had made specific claims about Mr Boyle and Mr Shamir that he felt needed to be corrected.

"It is something I would normally refrain from speaking about," Mr Jordan told Senate Estimates.

"But as the individuals in these cases have repeatedly sought out the public eye, and made public claims that are potentially damaging to our organisation and the administration of the tax system, I am obliged to respond in this way to ensure the facts are put on the table."

Mr Jordan referred to himself as the "chief tax collector", saying it was not a "particularly easy or popular role".

He said the ATO tried to act with "empathy when appropriate", but had a $45 billion-in debt book (debts owed across all taxpayer categories including collectible debt, insolvency debt and debt subject to objection or appeal), which would grow if the office did not move to collect money it felt was owed by taxpayers.

'We take whistleblowing seriously'

Mr Jordan said the ATO took "whistleblowing very seriously" and supported a culture of whistleblowing.

Since 2013-14, the ATO had 198 employees make public interest disclosures (PID), of which only 24 were substantiated.

He said 89 were unsubstantiated with no disclosable conduct found, and 79 were discontinued under Section 48 of the PID Act because they had already been investigated under other processes or could be, or "were vexatious, frivolous or did not concern serious disclosable conduct, or could be more appropriately investigated under another process".

Six are still under investigation.

Mr Jordan then went on to give specific details about the circumstances of the individuals, Mr Boyle and Mr Shamir, who both had appeared at Friday's hearing for the inquiry into the performance of the inspector general of taxation (IGT), which Mr Jordan did not attend, but other ATO officials did.

Mr Jordan noted Mr Boyle's case was currently before the courts but discussed it anyway, saying he was not facing criminal charges for being a whistleblower.

He said various media reporting, including Wednesday's story in the ABC, had conflated two separate issues — first about Mr Boyle's allegations of heavy-handed debt collection activities that were first raised in the joint Fairfax-ABC Four Corners report, and second that he was facing 66 criminal charges.

Mr Boyle is yet to face trial for the offences he has been charged with, including using a listening device to monitor a private conversation, recording another person's tax file number and disclosing protected information, but he plans to plead not guilty.

Mr Jordan said if the ATO had not taken action against these alleged breaches, this "would undermine public confidence".

Media exaggerating potential jail time, Jordan says

Mr Jordan also took issue with media commentary that Mr Boyle could face a maximum sentence of 161 years in jail, saying it was a "blatant and knowing mischaracterisation of our current sentencing system".

"The convention holds that sentences for similar, related offences are usually imposed concurrently rather than consecutively, having regard to the overall circumstances," Mr Jordan said.

He said the "disciplinary process for Mr Boyle was substantially completed before we knew anything about the alleged disclosure of taxpayer files".

In the case of the other whistleblower, Mr Shamir, Mr Jordan took the time to go into the taxpayer's history, noting Mr Shamir had stated "it was a coincidence that the day before I was marched out, the tax office had confirmed from the IGT that I had been issued with that notice".

"This is factually incorrect," Mr Jordan said.

"Our records show Mr Shamir was served the notice on 18 May. We were well aware of this notice on the 26th of May 2015 when Mr Shamir's lawyer advised the ATO that he had received the notice."

Mr Jordan said Mr Shamir had attended work but refused to perform his assigned duties for 10 days in the period before he was finally put on leave with pay on June 10, during which time he could have fulfilled the requirements of the Section 9 notice.

"This is an employee who was counselled over a number of years because of his persistent and inappropriate behaviour towards fellow employees and managers," Mr Jordan said, adding that on appeal the Fair Work Commission rejected Mr Shamir's unfair dismissal claim.

Labor senator Katy Gallagher called Mr Jordan's comments "extraordinary".

Centre Alliance senator Rex Patrick said some of the reporting about the two cases related to evidence given at parliamentary inquiries.

Mr Jordan also sought to give a detailed timeline of Mr Shamir's employment and the incidents that occurred.

Senate Estimates had to take a break to consider whether to table the report and decided it would not, and instead would give it to the inquiry into the IGT to examine.