In an interview last month, ASIO director-general Mike Burgess said if people escaping the conflict expressed "just rhetorical support" for listed terror group Hamas, but didn't have an ideology or back a violent ideology, they wouldn't automatically be barred from entering Australia.
Opposition Leader Peter Dutton in response called for a ban on allowing Palestinians into Australia until security vetting processes were strengthened.
In an interview to be aired on the ABC's 7.30, Mr Burgess said his previous comments had been misrepresented.
"I've watched with interest over the last couple of weeks how people have chosen to distort what I said," he said.
"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."
Prime Minister Anthony Albanese accused Mr Dutton of sowing division in the community, and pointed to civilians not being able to leave Gaza since May, after the Rafah crossing had been closed.
Opposition immigration spokesman Dan Tehan said Mr Albanese needed to clarify whether people who backed Hamas would be allowed into Australia.
"We were deeply concerned about the level of security checks which were taking place, it was unprecedented that people were coming from a war zone governed by a listed terrorist organisation on tourist visas," he told Sky News.
More than 1200 Israelis were killed when Hamas militants launched their October 7 attack.
About 40,000 Palestinians have been killed since Israel retaliated.
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