The flotilla activists were detained and assaulted by Israeli forces after attempting to deliver aid to Gaza.
The protesters called on the Australian government to impose sanctions on Israel, local media reported.
Demonstrators gathered in the Marble Foyer, kneeling with their hands behind their backs in a symbolic act meant to portray the detention of flotilla activists by Israeli authorities, ABC News reported.
They shouted “Sanction Israel!” and accused Prime Minister Anthony Albanese and Foreign Minister Penny Wong of being “complicit in genocide” as security officers escorted them from the building.
The protest follows a growing controversy over the treatment of activists involved in the flotilla.
Several activists, including Australians, have alleged mistreatment by the Israeli regime’s authorities, with accusations ranging from beatings to sexual assault during detention, Anadolu reported.
The issue gained wider attention after Israeli national security minister Itamar Ben-Gvir posted a video on social media last week appearing to mock detained flotilla activists while officers pushed and dragged some of them, drawing global condemnation.
The protest comes days after the Global Sumud Flotilla said that Israel had seized all 50 vessels attempting to reach Gaza by sea.
Turkey safely evacuated humanitarian aid volunteers from 41 countries, including 85 Turkish citizens who were part of the flotilla, the Turkish Foreign Ministry said late Thursday.
The flotilla, carrying 428 people from 44 countries, had departed earlier this month from the Turkish district of Marmaris in a renewed attempt to break the Israeli blockade on Gaza imposed since 2007, which has pushed most of the population to the brink of starvation.
In 2010, Israeli commandos raided the Turkish ship MV Mavi Marmara during a humanitarian aid mission to break the Gaza blockade, killing 10 Turkish citizens in clashes aboard the vessel.