Islamophobic incidents have surged more than six-fold over the past 21 months compared to a similar period before Hamas's attack on Israel on October 7, 2023.
More than 1500 incidents have been reported to the Islamophobic Register Australia in the period since the attack.
"We've seen deeply inadequate responses from governments, institutions, civil society," register co-executive director Sharara Attai told AAP.
About 1200 people were killed and 250 taken hostage when Hamas, a designated terrorist group in Australia, attacked Israel.
Israel's subsequent war in Gaza has killed more than 60,000 people, according to Palestinian health authorities.
The conflict has led to upswings in both Islamophobic and anti-Semitic incidents across Australia, including arson and graffiti attacks on places of worship.
But the federal government's response to the two issues had been unbalanced, Ms Attai said.
"The government is taking the issue of anti-Semitism seriously and rightly so," she said.
"The issue is that Islamophobia has not been treated with the same level of concern by government and by the media."
The register's latest report warned against the use of definitions of racism like the International Holocaust Remembrance Alliance definition of anti-Semitism, due to concerns it could be used to stymie criticism of the Israeli government and its actions.
Australia's special envoy to combat anti-Semitism, Jillian Segal, has recommended the definition be adopted across all levels of government and by public institutions.
"We need to see a principle of consistent commitment to combating all forms of racism ... and without weaponising any of these forms of racism to suppress legitimate political discourse," Ms Attai said.
The Islamophobia report found increasing levels of systemic issues targeting both Muslim and non-Muslim Australians who face reputational damage and professional exclusion for supporting Palestinian rights.
These include being uninvited from speaking engagements or being reprimanded or investigated for social media posts, such as wrongfully dismissed radio host Antoinette Lattouf.
"It's not just about talking about specific or isolated incidents," Ms Attai said.
"There is an entrenched pattern."
The report also called out a rising level of force used by police at protests, and Islamophobic and anti-Palestinian racism being ignored or minimised by authorities.
The Islamophobia register is a not-for-profit that has collected hate incident data for more than a decade, working in partnership with Australian universities and Islamic community groups.
"What we're seeing is not just a spike in anti-Palestinian incidents," Palestine Australia Relief and Action founder Rasha Abbas said.
"It's a systemic tolerance of the suppression of voices calling for justice and human rights."
Meanwhile, tough anti-protest laws in NSW and similar legislation under consideration in Victoria were a worry for all Australians, independent researcher Naser Alziyadat said.
"What is truly alarming is the systemic erosion of the democratic values that Australia has long cherished," Dr Alziyadat said.
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