Mr Porter strongly denies the allegations.
Acknowledging the rallies in parliament on Monday, Mr Morrison praised Australia's "vibrant liberal democracy".
"It is good and right, Mr Speaker, that so many are able to gather here in this way, whether in our capital or elsewhere, and to do so peacefully to express their concerns and their very genuine and real frustrations," Mr Morrison said.
"Not far from here, such marches, even now, are being met with bullets. But not here in this country.
"This is a triumph of democracy when we see these things take place."
Reacting on Twitter, Labor MP Julian Hill said the prime minister was "so out of touch it's astounding", while Greens leader Adam Bandt described his comments as "unbelievable".
Labor leader Anthony Albanese in parliament accused Mr Morrison as having "not so much a tin ear, as a wall of concrete", and called for an independent inquiry into the allegation against Mr Porter.
"The prime minister needs to listen, to listen to what women are saying about what is happening in this building and outside," Mr Albanese said.
"What I saw outside was passionate. Women who are angry, they are angry about what's happened to them, they are angry about what's happened to their mothers, their grandmothers, their sisters, their daughters and their granddaughters.
"They are crying out that this is a moment that requires leadership, and it requires leadership from this prime minister."
Mr Morrison said those who gathered on Monday did so out of a sense of deserved frustration, and said he shared the same concerns.
"The government understands and shares the frustrations of women and men across this country who want to see women safe in their workplace, want to see them safer in our community, they want to see them safer in this building," he said.
"This is Australia's ambition, this is my government's ambition ... and I look forward to achieving a unity of purpose across this chamber and the other."
Senator's statement 'should never have been uttered'
Mr Morrison also intensified his criticism of Defence Minister Linda Reynolds, blasting her "disgraceful slur" against alleged rape victim Brittany Higgins.
Senator Reynolds will have to pay compensation to the former Liberal staffer after calling her a "lying cow".
The minister, who is on extended medical leave, apologised and retracted the remark, which was leaked from her office.
In his strongest comments yet, Mr Morrison on Monday said he was pleased the "disgraceful slur" had been withdrawn.
"Of course she should never have said it," he said.
But the prime minister challenged Labor MPs to provide transcripts of what was said in their offices before being in a position to "cast stones".
"This was a statement that should never have been uttered, whether in a private office or elsewhere," Mr Morrison said.
Ms Higgins says she was raped at Parliament House by a colleague in 2019 when she was working for Senator Reynolds.
The minister has argued she made the comment in response to suggestions she didn't offer her former employee enough support at the time of the alleged incident.
Ms Higgins will donate the undisclosed sum to sexual abuse survivors counselling and support in Canberra.
The prime minister has defended keeping Senator Reynolds in the defence portfolio despite growing calls for her to be sacked.
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.