Speaking after handing down his annual threat assessment earlier this week, ASIO Director-General Mike Burgess said both Islamophobia and anti-Semitism were wrong, but the agency was investigating the latter more.
"It's clear that actually right now, we are seeing way more anti-Semitism in terms of significant incidents," he told ABC's Radio National on Friday.
"On the threat to life, our number one priority now is investigating anti-Semitic acts in this country."
The nation has experienced escalating attacks since December, when a Melbourne synagogue was firebombed, homes and cars vandalised and Jewish cultural institutions targeted.
Mr Burgess said if behaviours were left unchecked, they became reinforced and gave others permission to do the same, if not more.
"We've seen attacks on Jewish-Australians move from intimidation and general harassment through to direct targeting of people, places of worship and communities. It defies logic. It's unacceptable," he said.
"We've got to have a hard response so people know those behaviours, which don't represent the country, are unacceptable in our country and will not be tolerated."
The Albanese government has faced increasing criticism over its handling of anti-Semitism.
Mr Burgess urged restraint when discussing the attacks and broader issue, vowing police would get to the bottom of the incidents.
"The police are doing a fantastic job, and personally - not that what I want matters here - but I wish people would just let the police do their job and stop commentating from the sides," he said.
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