"I don't think people should be coming in from that war zone at all at the moment," the federal opposition leader told Sky News on Wednesday.
"It's not prudent to do so, and I think it puts our national security at risk."
Government and intelligence agencies say all visa applicants undergo thorough security vetting.
There have been 2922 visas granted between October 7 and August 12 and 7111 refused for people with Palestinian Authority documents, according to Home Affairs Department figures.
During the same period, 8746 visas were granted to Israeli citizens and 235 were refused.
The PM questioned Peter Dutton's faith in the same vetting processes in place under the coalition. (Mick Tsikas/AAP PHOTOS)
Home Affairs Minister Tony Burke said it was proof the security vetting system was working and security agencies were doing their jobs.
ASIO was involved with the visa process "whether you come from the United States or whether you come from the Gaza Strip", Mr Burke told parliament on Wednesday.
Prime Minister Anthony Albanese questioned Mr Dutton's faith in Australia's intelligence agencies and the same visa vetting processes in place under the coalition government.
Coalition members peppered government ministers in parliament for guarantees no visas were granted to supporters of the designated terrorist group Hamas, which attacked Israel on October 7.
"I have confidence in the work that our security agencies do, they work their guts out to keep us safe," Mr Albanese said.
"If the leader of the opposition doesn't have confidence in that system, he should say so."
Australia Palestine Advocacy Network president Nasser Mashni blasted Mr Dutton's comments and called for them to be condemned.
They were "another glaring example of the abhorrent and increasingly normalised brand of racist politicking designed to stir up fear and hatred against the Palestinian people", he told AAP.
Gazans are "human beings ... trying to survive", minister Jason Clare said.
"Anybody with a brain, anyone with a heart, would be saying, this war needs to end ... the killing and the slaughter of innocent people need to stop, the starvation of kids needs to stop," he said.
Australia should do more in one of the worst humanitarian disasters of our time, David Pocock says. (Mick Tsikas/AAP PHOTOS)
Save the Children CEO Mat Tinkler and independent senator David Pocock accused the opposition of hypocrisy after supporting Ukrainians and Afghans leaving war zones.
The same streamlined humanitarian visa class used for Ukrainians and Afghans has not been opened to Palestinians.
Seven onshore protection visas have been issued to Palestinians between October 7, 2023 and June 30.
"Australia needs to be doing more, not less, to support people seeking to flee one of the worst humanitarian catastrophes of our time," Senator Pocock said.
Shadow attorney-general Michaelia Cash rejected claims of hypocrisy over the coalition government helping people flee Afghanistan when the Taliban took over, saying all appropriate security checks were carried out.
People in Gaza cannot leave with the Rafah crossing closed.
About 1200 Israelis were killed when Hamas launched its October 7 attack and almost 40,000 Palestinians have been killed because of Israel's counteroffensive in Gaza.
The federal government has called for a ceasefire plan to be adopted as the death toll mounts and the humanitarian situation worsens.
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