Morrison told parliament on Thursday that "these issues are obviously deeply concerning and I know deeply distressing, for Ms Miller, minister Tudge and the families affected by these events".
He added that while Tudge had denied the allegations, the "seriousness of the claims" meant it was important for the matters to 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, through an independent and fair process, to ensure that the matters that have been raised can be properly assessed and the views put by the respective parties in relation to these issues."
Morrison confirmed he asked Tudge to step aside while the allegations are investigated by an independent review, which will be run by the Prime Minister's department.
Miller worked as Tudge’s press secretary when he was the Minister of Human Services.
She called out the toxic workplace culture of parliamentarians in the wake of the review's release this week.
"The Liberal party doesn’t have a women problem. It has a men problem," she said.
"I’m not here because I want to be but because speaking through the media is the only way that this government will listen. All of us who have survived awful experiences in this workplace tried to reach out and seek change many, many times before we went to the media. This is our last resort."