ASIO director-general Mike Burgess courted controversy after saying if people escaping the conflict expressed "just rhetorical support" for Hamas, but didn't back a violent ideology, they wouldn't automatically be barred from entering Australia.
In response, Opposition Leader Peter Dutton called for a ban on Palestinians entering Australia until vetting measures were strengthened.
Mr Burgess said his initial comments had been skewed.
"I've watched with interest over the last couple of weeks how people have chosen to distort what I said," he told the ABC.
"I said that if you support a Palestinian homeland that may not discount you because that by itself is not a problem.
"But I also said if you have a violent extremist ideology, or you provide material or financial support to a terrorist organisation, that will be a problem."
Peter Dutton accused the government of putting ASIO's chief in a "difficult position". (Lukas Coch/AAP PHOTOS)
Anthony Albanese accused the opposition of undermining Australia's top spy.
"Mike Burgess does a great job and people, including the coalition, should back him in," the prime minister said.
"He has my total confidence."
Mr Dutton said he welcomed the "clarification" from the ASIO boss.
He called on Labor to apologise to Mr Burgess for putting him "in a difficult position".
"When you bring people in from a war zone controlled by a terrorist organisation, you can't issue tourist visas," Mr Dutton told reporters.
At least 41,000 people have been killed in Gaza since Israel declared war on Hamas following the terrorist organisation's October 7 attacks.
More than 2900 Palestinians have been granted Australian visas since the war began, with about 7000 other applications refused.
During the same period, 8746 visas have been offered to Israeli citizens, with 235 requests knocked back.
Gaza's last exit point, the Rafah crossing, has been closed to civilians since May.
John Coyne, from the Australian Strategic Policy Institute, said every visa application should be judged on its merits.
"Every case where there is any sign of risk, a risk assessment should be undertaken by relevant authorities," he told AAP.
"That risk assessment should be undertaken free of politics and should be undertaken by law enforcement and appropriate border migration officials."
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