Australia Human Rights Commission president Hugh de Kretser was among several witnesses who teased out the distinction before the inquiry body on Monday.
It was the first day of a block of hearings in Melbourne exploring the experience of Jewish students and academics, including efforts by their institutions to combat hate.
Mr de Kretser said delineating between legitimate criticism of Israel and anti-Semitism could be "complex".
"(There has been) public controversy around where to draw line in terms of criticism of Israel and where it's racism or where it is it anti-Semitic," he said.
"If you're if you're denying people opportunities, if you're racially harassing them, if you're abusing them, if you're threatening them, that is racism."
But the university setting had "unique aspects" and complexities in determining what was anti-Semitic given academic freedoms, he said.
"I think the way anti-Semitism is playing out, the way anti-Palestinian racism, Islamophobia is playing out in Australia, creates particular tensions in particular sectors."
Professor Josh Keller, representing the Australian Academic Alliance Against anti-Semitism, said critics of the Netanyahu government were not necessarily anti-Semitic.
"I share some of those criticisms," he said.
But anti-Semitism arose when prejudice extended to the way "people talk about or feel or act about the Jewish people living in Israel", he said.
He spoke of a sticker on a university campus that featured the Star of David and the phrase "we stand with baby killers".
"When you're calling a group of people baby killers, that is not only not true, it's invoking the most immoral act that any human being could possibly do," he said.
He argued the complexities of anti-Semitism mean it required its own basket of legislative protections distinct from other kinds of vilification.
The royal commission is using the week to focus on anti-Semitism and other hate in university settings, including interrogating the intersection between criticism of Israel and Jewish students feeling unsafe.
From Monday, the government will strengthen university governance standards, including a requirement that institutions adopt anti-racism standards with definitions on anti-Semitism, Islamophobia and racism towards Aboriginal and Torres Strait Islander people.
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