Scott Morrison has indicated both ministers will still feature on his frontbench line-up, with the reshuffle expected within days.
This is despite the Prime Minister repeatedly admonishing Senator Reynolds for her "disgraceful" response to the alleged rape, when she called Ms Higgins a "lying cow".
Home Affairs Minister Peter Dutton, who is likely to replace her in the defence portfolio, denied Mr Morrison was afraid to sack her.
"I don't think the PM is afraid to sack anyone if they've done the wrong thing," Mr Dutton told the Nine Network on Friday.
He said Senator Reynolds had done an outstanding job in defence and provided what she believed was enough support to Ms Higgins.
Mr Dutton also dug in behind the embattled Attorney-General.
"The Prime Minister has been very clear that he wants them to remain in cabinet and I think that's appropriate," he said.
Talking to Nine's A Current Affair on Thursday night, Mr Morrison dug his heels in on his defence of the Attorney-General, again labelling him "an innocent man" and rejecting the idea that he could instigate a non-criminal inquiry into a historical rape allegation about him.
"That's a job for the police. If they believe it should be," he said on Thursday night.
Mr Porter, currently on mental health leave, has strenuously denied the allegation.
The defence minister is on medical leave with a coronary condition after calling alleged rape victim Brittany Higgins a "lying cow".
Mr Morrison, who described the term as "disgraceful", said Senator Reynolds' condition was exacerbated by the "distress she was under" in parliament.
"That has had a further effect on her physical health. And so we're still talking to her doctors and her, with her permission. And we're working through that with Linda now in terms of what duties she can perform."
The prime minister declined to say when both ministers' future roles would be confirmed.
"They will continue to play a very important role in my cabinet," he said.
"When I make judgements about those things I'll announce them," he added.
Mr Morrison added he would be "very pleased" to meet with Ms Higgins if she wishes, while admitting he has failed to fully grasp the problem of sexism before now.
He said that he doubted the former government staffer would wish to discuss something "as deeply private and personal" with him as her alleged rape in Parliament House by a colleague, but that she would be "very welcome" to.
Ms Higgins' story had triggered "one of the most hard and deeply personal, confronting conversations I have seen take place here", Mr Morrison said.
He said he often heard statistics about violence against women but Ms Higgins' story had taken him "deeper into this issue" than he had appreciated before.
"We have gone way deeper, we have gone beyond the sheer shock of violent acts. We are starting to deal with some home truths," he said.
The interview aired hours after Ms Higgins made a formal complaint to Mr Morrison's chief of staff, asking him to investigate whether anyone in the prime minister's office tried to privately undermine her loved ones.
Mr Morrison has ordered an inquiry into whether any of his staff did provide negative information to journalists on Brittany Higgins and her close supporters.
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He has said he triggered the process after his chief of staff received confidential information from a "primary direct source" with knowledge of the claims.
"As I said in parliament when this was suggested, this is not something I would ever condone," the prime minister told A Current Affair.
He defended himself against the accusation that he is late to the issue of sexism, saying that while women "live with it every day", he has had different experiences.
"For many Australians, this has been like a big wake-up call and it's been like a red light to say, stop, look, listen' and that's what we're doing," he said.
He said that "many things...will make our country stronger to deal with these issues" including the need for respect towards women.
"Equally, our courts, our police, our justice systems, they are also important. We can't dismiss that and think we are fixing that problem," he said.
He called for greater respect in Australian society, including on how people disagree "on this type of issue".
With reporting by AAP.
If you or someone you know is impacted by sexual assault, you can call 1800RESPECT on 1800 737 732 or visit 1800RESPECT.org.au.