Bruce Lehrmann's defence lawyer was "pissed off" by suggestions during the high-profile trial that his cross-examination of Brittany Higgins had been coached by a former coalition minister.
He also rejected allegations made by Director of Public Prosecutions Shane Drumgold about police interference in the criminal justice process.
Steven Whybrow is the second witness to give evidence to an independent inquiry into how the justice system handled Ms Higgins' rape allegations.
The inquiry, led by former Queensland solicitor-general Walter Sofronoff, is examining the actions of ACT police, prosecutors and a victim support service during the investigation and trial.
In a letter to Chief Police Officer Neil Gaughan after the trial was derailed, Mr Drumgold alleged Liberal senator Linda Reynolds had "engaged in direct coaching of the defence cross-examination of the complainant".
Mr Whybrow said he did not know about the letter before parts of it were published by the Guardian following a freedom of information request.
He told the inquiry it was an "appalling mischaracterisation" of what had happened.
"I don't hold a candle for Senator Reynolds but (the suggestions) were unfair and, as far as I was aware, untrue," he said.
During the trial, Mr Whybrow told Mr Drumgold he had been contacted by the senator asking for transcripts from proceedings to be sent to her lawyers.
Mr Drumgold confronted Senator Reynolds about this while she was in the witness box and also questioned why her husband had been sitting in court for the proceedings.
"I showed (Mr Drumgold) that she wasn't getting the transcripts and that I had positively suggested to her not to have any conversations with her husband," Mr Whybrow said.
"He put these positive things to Linda Reynolds, including that she was trying to tell me how to do my job and give me cross-examination tips.
"I was pissed off, I was angry and I wrote ... to (Mr Drumgold) about what I considered was improper conduct."
The defence lawyer also said he was "flabbergasted" to learn Mr Drumgold had read Ms Higgins' sensitive counselling notes, which had been provided to both sides of the case by the police in error, but had not been read by the defence team.
"It's not an even playing field. The prosecution has material in its possession that the defence does not," Mr Whybrow said.
Mr Lehrmann was tried by the ACT Supreme Court but the case was derailed because of juror misconduct.
Prosecutors later dropped the charges against him because of fears about the impact a second trial would have on Ms Higgins' mental health.
Mr Lehrmann denies raping Ms Higgins in Parliament House in 2019.
But Mr Whybrow believed the statement made by Mr Drumgold when he dropped the charges conveyed a suggestion about Mr Lehrmann's guilt.
"The DPP is not the solicitor for the complainant. He is supposed to be the objective minister of justice," he said.
"He could have said something as well, if he wanted to, about this being very difficult for Mr Lehrmann who has had his life turned upside down for the last two years and will now not get an opportunity to clear his name."
Mr Drumgold called for a public inquiry because of what he believed was a "passion" from investigators for the prosecution to fail.
But Mr Whybrow disagreed with Mr Drumgold's assessment of police behaviour.
"This was not a case where (the defence) at any stage thought the police were in any way trying to undermine this investigation," he said.
"(Police) looked at everything, whether it suited the allegation or it suited the statements made by Mr Lehrmann in their record of interviews."