Tax Commissioner Chris Jordan has undermined trust in Parliament by using parliamentary privilege to discuss the affairs of individuals, according to some senators sitting on the committee which heard Mr Jordan's estimates testimony on Wednesday.

Key points: Tax commissioner Chris Jordan's opening statement to Senate Estimates on Wednesday has angered some senators

Tax commissioner Chris Jordan's opening statement to Senate Estimates on Wednesday has angered some senators Centre Alliance senator Rex Patrick and Greens senator Peter Whish-Wilson say Mr Jordan did not act responsibly

Centre Alliance senator Rex Patrick and Greens senator Peter Whish-Wilson say Mr Jordan did not act responsibly Mr Jordan stands by his comments, having felt a need to address "unbalanced depiction" of the ATO by former employees and the media

The ATO boss took the extraordinary step of using his opening address at Senate Estimates to talk in detail about the employment affairs of two former employees, Richard Boyle and Ron Shamir.

Senators Rex Patrick and Peter Whish-Wilson who were part of the Senate Estimates hearing where Mr Jordan made the comments, told ABC News they felt what Mr Jordan did had undermined the institution of Parliament, and feared it could deter other whistleblowers from coming forward.

Mr Jordan had alleged both former employees had not been terminated due to their whistleblowing activities but had been the subject of "ongoing workplace performance or conduct issues".

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

An ATO spokesman told ABC News Mr Jordan stood by his opening address to Senate Estimates.

"He was compelled to address the irresponsible allegations that have been made repeatedly over a number of months," the ATO spokesman said.

"The public commentary on our treatment of whistleblowers was reignited by individuals appearing last week at the Senate hearing into the performance of the inspector-general of taxation, and earlier this week when the ATO was made the focus of the broader 'your right to know' campaign launched by several media outlets.

"The commissioner was concerned that much of this public commentary is misleading, unbalanced, and at times simply untrue."

Senator Patrick calls it an 'abuse of parliamentary privilege'

But Centre Alliance senator Rex Patrick said discussing a private individual's affairs at Estimates was "highly irresponsible" and "an abuse of parliamentary privilege".

"It goes against his [Mr Jordan's] judgement," Senator Patrick said.

"Grandstanding the issues at Senate Estimates, which are proceedings designed to deal with other matters, was inappropriate."

He noted that Mr Boyle and Mr Shamir not having the right of reply at that Senate Estimates forum was problematic.

Directly after Mr Jordan's testimony, Greens senator Peter Whish-Wilson requested the secretariat of the Senate Economics Legislation Committee have the senators sitting on the committee consider whether Mr Jordan's opening statement could be expunged from the Hansard record.

Senator Whish-Wilson requested this happen given information provided by Mr Jordan "went beyond what was public knowledge", was subject to pending court proceedings, and the individuals named had no immediate right of reply.

While the committee is considering the request, ABC News understands it is unlikely to happen.

"Irrespective of that, it's impossible to unhear what was heard," Senator Patrick said, noting widespread media reporting of Mr Jordan's comments at the Estimates hearing.

He said the current inquiry into inspector-general of taxation would have been a better forum for Mr Jordan to raise his concerns.

Centre Alliance senator Rex Patrick said ATO boss Chris Jordan should have exercised his judgement. ( ABC News: Tamara Penniket )

'It looked petty to me', Senator Whish-Wilson says

Senator Whish-Wilson said he was concerned Mr Jordan had damaged Parliament's reputation by using the Estimates hearing to attack individuals, where they did not have a right of reply.

"Mr Jordan gets paid big bucks to be one of the country's most senior bureaucrats and what he did looked petty to me," Senator Wish-Wilson said.

"It did reputational damage to the Senate yesterday [on Wednesday]."

Greens senator Peter Whish-Wilson is worried whistleblowers may be deterred from coming forward. ( ABC News: Adam Kennedy )

Senator Whish-Wilson said in all his time in Parliament, he had never seen such behaviour from a senior and "powerful" public servant.

"There was a general feeling of anger amongst the [Senate Economics Legislation] Committee," Senator Whish Wilson said.

"Chris Jordan has thrown a hand grenade and we are all going to be feeling the shrapnel."

He said the Senate Estimates process was the "jewel in the crown" and there were strict processes in place to make sure the institution was trusted.

But he felt people watching Mr Jordan's attack on individuals could now be deterred from coming forward.

Labor senator Katy Gallagher, who also was at Wednesday's estimates hearing, said she found Mr Jordan's comments "extraordinary".

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

Mr Boyle is yet to face trial for the offences he has been charged with, which include 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.

The ATO spokesman said given the "serious nature" of public allegations the whistleblowers had made about the ATO, the "commissioner found it necessary to address the unbalanced depiction of our organisation".

"He wanted to reinforce to the public and his staff that he will not tolerate our activities being misrepresented," the spokesman said.