The accusation comes as Labor called for talks on a new framework to improve working conditions in Parliament House.

Rachelle Miller says she was punished because of her affair with another cabinet minister, Alan Tudge, who she had worked for previously.

Ms Miller has accused Senator Cash of months of poor treatment during the first half of 2018.

The complaint says Ms Miller felt ambushed in April 2018 with a request to go on leave, was asked whether personal issues were undermining her work, and was excluded from meetings.

In June 2018, Ms Miller was told the office was being restructured and her role would be made redundant.

Ms Miller was told she could apply for a more junior role.

"It was very clear that this was a fake redundancy process put in place to get rid of me from the office," she wrote in a complaint to the Department of Finance.

"There were no grounds for this, there had been no performance management process put in place, nor had I received formal warnings."

Senator Cash denies Ms Miller's claims.

"The minister strenuously rejects claims of any adverse treatment of Ms Miller by her, or her office, and strongly disputes Ms Miller's version of events," a spokesman told AAP.

"At the time of her employment, between late 2017 and mid-2018, the minister and the office understood Ms Miller's personal circumstances which is why support, leave and flexible work arrangements were offered to her.

"Given the matter is now subject to a formal process in the Department of Finance, the minister will not be commenting further."

Ms Miller has lodged a separate complaint against Mr Tudge, accusing him of bullying and intimidation.

She now works in the private sector.

Mr Tudge's spokesman said he was not aware of any previous complaint and directed further enquiries to the finance department.

Labor frontbencher Katy Gallagher told the Senate there were people working in Parliament House that have not found it to be a great workplace at times and the issue should not be swept under the carpet.

"I actually think there's a more serious discussion that we should be having and we should be taking the lead on - not necessarily us as women, but all of us in this place who employ people," she said.

"Where there are outliers (who treat staff badly), we need to be dealing with that and putting in place a framework that ensures that this workplace is the best in Australia and sets the highest standards."

The Greens have called for an independent parliamentary standards commissioner to receive and investigate complaints.

"The existing complaints process is little known and far too weak," Greens senator Larissa Waters said.

Australian Associated Press