During the investigation, Parliamentary Service was also told about alleged issues around political work, but it is unclear if it investigated further.
Previously, Auditor General Kevin Brady investigated claims that parties were using parliamentary funding for political advertising - finding parties unlawfully spent $1.17 million on what he deemed to be political advertising.
The staffer in this case gave what he believed were examples of similar transgressions.
Those included staff writing Barry's column "Maggie's Messenger", where she encouraged people to vote for Northcote MP Dan Bidois, and completing a "Super Blues" brochure for an over-60s National Party conference.
The staffer said some weeks, up to half his work was party work. He told the Herald he felt uncomfortable with the work, because he knew it was against the rules but felt unable to say no out of fear of losing his job.
Parliamentary rules strictly stipulate party work is not part of support staff's job.
According to her interview with investigators, Barry also knew it was against the rules.
However, in a recording obtained by the Herald, Barry said the opposite to the staffer the day he was due to give evidence for his co-worker's personal grievance case.
In it she said writing brochures on office time was "legitimate", while acknowledging the investigators would not be impressed if they found out.
"It's how the world goes around," she said. "You know the lay of the land."
The Herald has also seen messages from Barry - who rarely used email but instead spoke into the voice-to-text function on her phone - appearing to request political work be completed during office hours.
Yesterday, Barry conceded that her parliamentary staff have done National Party work, but it was in their own time and using their own email addresses.
"I never asked parliamentary staff to do party work," she said.
"I've been a Member of Parliament for more than seven years. I definitely understand the distinction."
She also said a workplace investigation cleared her of bullying charges. However, the former staffer said no findings at all were made in his case with regards to bullying.
The Herald has been unable to confirm the result of the other case, which was a personal grievance.
Electoral law expert Andrew Geddis said that MPs pressing their staff into doing political work gave them a far greater advantage in elections than non-MPs and the situation may need closer scrutiny.
"Taxpayer funding to hire MPs' staff is given so that they can do their jobs as elected representatives, not to help them win re-election," said Geddis, a professor of law at Otago University.
"If it gets misused for party purposes, sitting MPs get a massive advantage against their unfunded challengers."
After Brady investigated in 2005, most parties repaid the funds but Parliament also changed the rules so that in future, the types of expenditure previously found to be unlawful, came within the rules.
Only advertising explicitly seeking or discouraging support for a party or candidate or explicitly seeking funds cannot not be paid by Parliamentary Service.
The bullying allegations and the complaint to the Auditor General follows an independent review into bullying and harassment at Parliament launched by Speaker Trevor Mallard last week.
Simon Bridges confirmed today he knew about the Auditor General investigation.
Bridges said he stood by Barry and said Parliamentary Service had no made finding of bullying or harassment.
"She is a hard-working effective MP. My understanding now is there is an Auditor General investigation. While I'm not concerned about it, it's not appropriate for me to comment."
He said it wasn't necessary to stand down Barry while the investigation took place.
