The prime minister made the comments while comparing nationwide rallies to violent protests in Myanmar.
"This is a vibrant liberal democracy," Mr Morrison told parliament.
"Not far from here, such marches, even now, are being met with bullets, but not here in this country."
Minister for Women Marise Payne defended his remarks.
"The observation about the opportunity to protest peacefully and safely in Australia is an important one," she told reporters in Canberra on Tuesday.
"Our democracy does provide Australians with that opportunity."
But Labor senator Malarndirri McCarthy described the comments as deeply disappointing.
"What happened in the parliament yesterday sent a deeply depressing, disturbing and disappointing message to Australians," she told Nine.
Australian Council of Trade Unions secretary Sally McManus, who addressed a rally in Canberra on Monday, said the prime minister's comments were shocking.
"I really question whether he actually gets it, whether he actually really understands how at least half of the population and probably more feel at this moment," she told the ABC.
"We feel as though enough is enough, we want change."
Ms McManus said the movement was focused on violence towards women, children and some men.
"The fact that he would then say, 'Well, if you were at a rally elsewhere, you would get shot', it was tone-deaf, just completely out of step with the feeling," she said.
"It would be much better to listen, to have empathy, to understand and to act."
Senior ministers have defended Mr Morrison's decision not to attend the march for justice outside Parliament House. But independent senator Jacqui Lambie said the prime minister should have shown up.
"He should have shown some courage and he should have stood in front of those women and their husbands and their sons, and he should have stood there and he should have taken it," she told Nine.
"That's how it is. That's life."
Tens of thousands of people rallied across the country demanding action from leaders on gendered violence.
Former Liberal staffer Brittany Higgins, who alleges she was raped by a colleague inside a ministerial office in 2019, spoke at the event in Canberra.
Treasurer Josh Frydenberg defended his own absence at the march.
"Well, I didn't go to the march because the prime minister offered a meeting to the leaders of that march and they turned him down, and I think that was unfortunate," he told Sky News.
"But I think yesterday was a powerful moment outside the parliament.
"Attention was brought to a very important issue, an issue that we take very seriously, an issue that we're acting on, namely domestic violence, sexual violence against women.
"We must do better, we will do better as a nation in tackling this scourge."
The government has committed to take up demands raised as part of the rally's petition, including an inquiry into gendered violence and the full implementation of recommendations from sexual harassment report.