Department secretary Rob Stefanic instead told senators workplace morale had significantly improved for Parliament House staff, though there was still "room for improvement", in a Senate committee hearing held on Friday.

He also addressed allegations by the Community and Public Sector Union that staff had felt intimidated and bullied by senior management, claiming they were "simply not accurate" - a point the union has defended against.

"Like every organisation, we have a marginal cohort of staff that behave inconsistent with the code of conduct and values," Mr Stefanic said in his opening statement on Friday morning.

"Misconduct in various cases was proven to be dishonest, disrespectful, bullying, threatening, and even unlawful.

"This cohort dishonestly recast themselves as victims and whistleblowers, and they are not concerned to give false evidence to a parliamentary committee."

Survey data included in the union's submission to the committee showed three-quarters of department staff who responded had experienced bullying within the workplace.

Liberal senator James Paterson questioned the validity of the surveys the union had conducted, adding the union's survey sample size was not large enough to be reliable.

He added the union's evidence appeared to be "false" and would need to be scrutinised further.

Union deputy secretary Beth Vincent-Pietsch hit back at the claims, noting the secretary had himself conceded workplace culture needed further improvements.

"The two DPS security surveys in the CPSU submissions had a participation rate of 20-25 per cent," Ms Vincent-Pietsch told The Canberra Times on Tuesday following Senator Paterson's accusations.

"While that is not all staff, it is a significant portion that even if the only people who are concerned [about], or experiencing toxic workplace culture, are the ones doing our survey that would still be a significant problem.

"Given the seriousness of the concerns raised, any staff expressing these concerns should be listened to [and] not dismissed by political grandstanding by Liberal senators."

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The union had earlier accused department heads of "weaponising" disciplinary action - including code of conduct complaints - to silence staff.

The claim was levelled in a second submission to the parliamentary inquiry examining the department, which details ongoing concerns among staff about bullying, harassment and "cover-ups" inside their workplace.

The union first lodged a submission in December, but received further feedback from its members after the Brittany Higgins rape allegations shone a spotlight on Parliament Houses' workplace culture.

The submission highlighted the case of security guard and union member Nikola Anderson, who chose to speak to Four Corners about her actions on the night of Ms Higgins' alleged rape because she feared she was poised to lose her job or be scapegoated by the government.

The union said Ms Anderson was right to be concerned because security staff were "frequently" threatened with disciplinary action, including being slapped with code of conduct complaints or losing their job, if they spoke out.

While code of conduct complaints were used to change the department's culture over the years, Mr Stefanic said, they had not been used to the level the union had alleged.

"The key component of our culture change program has been to address behaviour that is not consistent with the Parliamentary Service Code of Conduct, and the Parliamentary Services Values," he told the hearing.

"The data shows that codes are used sparingly, and terminations are extremely rare."

The latest dispute follows a long-standing row between the department and the union in light of a number of allegations occurring within Parliament House over the years.

An open letter, signed by union members within the department along with the Department of the House of Representatives, the Department of the Senate, the Department of Finance and the Parliamentary Budget Office in March, made demands to senior management to introduce better working conditions.

It asked for improved complaints processes and reporting mechanisms, mandatory training and greater protections for workers within workplace agreements.

It followed revelations revealed earlier this year, including the allegation by Ms Higgins and reports of political staffers taking and sharing explicit images.

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