Brittany Higgins with Prime Minister Scott Morrison.
Prime Minister Scott Morrison earlier on Thursday said the under-fire senator "deeply regretted" the remarks.
"I appreciate that it has been a stressful time but that sort of behaviour and language is never excusable".
Senator Reynolds released a statement on Wednesday saying she had not cast doubt on Ms Higgins' allegations which were "very serious", Senator Reynolds said.
The Prime Minister told parliament it was unacceptable he had not been informed immediately.
Ms Higgins has told local media she felt unsupported by her boss and pressure that she would lose her job if she reported her alleged rape to police.
"She's gone this morning".
Independent MP Zali Steggall said: "It makes her position all the more untenable".
The Defence Minister has apologised to staff for the remarks which she said had been made during "a stressful time".
The letter also noted that while Reynolds has apologised to her staff, she has not not actually apologised to Higgins herself about the comment.
Senator Reynolds, who is on medical leave following heavy criticism of her handling of the allegation, is under increasing pressure to resign.
The PM asked for understand for Senator Reynolds
"A report in The Australian attributed some remarks to me regarding the very serious allegations made by my former staff member, Ms Brittany Higgins, " she said in a statement.
"I have never questioned Ms Higgins account of her alleged sexual assault and have always sought to respect her agency in this matter".
"I did, however, comment on news reports regarding surrounding circumstances that I felt had been misrepresented", she continued.
Ms Higgins has alleged she was raped by one of Ms Reynolds' ex-advisers - a charge that has rocked the government. "I welcome her decision to progress this matter with the Australian Federal Police", she said in the statement.
However, Higgins publicly said that the "incredibly hurtful" comments were just "further evidence of the toxic workplace" inside Parliament House.
The alleged sexual assault took place in March 2019, but Ms Higgins only went public with her claim last month. The woman took her own life a year ago.
When contacted by SBS News about possible legal action, a spokesperson for Senator Reynolds said: "The Minister has no further comment to the statement issued last night".
Last week, Senator Reynolds was admitted to hospital with a pre-existing medical condition and forced to cancel a much-anticipated speech at the National Press Club - where she was expected to be pressed on her handling of the alleged incident. But equally, there have been others who have been drawn into this.
Defence Minister Linda Reynolds did not deny calling Brittany Higgins a "lying cow".
When asked by a reporter point blank if he had "slept with" the alleged victim, Mr Porter said: "I did not sleep with the victim".
Mr Porter has not been charged and is not the subject of any ongoing current police investigation. And what is - I would just simply say to people - you know, it's been a very traumatic several weeks for many people.
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