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The minister, Alan Tudge, was accused on Thursday of physically and emotionally abusing his former press secretary Rachelle Miller.
Mr Tudge said he "completely and utterly rejects the allegations" and that relationship - which occured in 2017 - was consensual.
Australia’s prime minister, Scott Morrison, said Mr Tudge had agreed to stand aside while an investigation got underway.
"It’s important these matters be resolved fairly and expeditiously. To this end, the minister has agreed to my request to stand aside while these issues are addressed by my department," Morrison told Australian lawmakers.
"I wish to stress that this action in no way seeks to draw a conclusion on these matters... but this is the appropriate action for me to take under the ministerial standards.”
Ms Miller said on Thursday that there had a “significant power imbalance” in the relationship with Mr Tudge.
"The bullying, intimidation, harassment I experienced from him at work completely destroyed all of the confidence I had in my ability. I did not believe I’d find a job anywhere else. I was breaking down in tears regularly," she said.
This comes just days after an independent inquiry found that a third of people working in Australia’s parliament have experienced sexual harassment.
Mr Morrison, who ordered the review in February after his party came under pressure over its handling of an alleged rape inside the building, said on Tuesday that the findings were “appalling” and “disturbing”.
Support for his conservative coalition government fell in the wake of the rape allegation, while thousands of women marched across the country calling for greater equality.
The report made 28 recommendations, including greater gender balance among both lawmakers and their staff, new alcohol policies and the creation of a new human resources office to deal with complaints.