She shouted: “Give us our land back. Give us what you stole from us! Our bones, our skulls, our babies, our people. You destroyed our land. Give us a treaty!
“You are not our King, you are not sovereign… you have committed genocide against our people.”
Security stopped her getting close to the monarch and ushered her out the chamber in Canberra.
Ms Thorpe told Breakfast with Kay Burley she stood by her actions.
“We are the real sovereigns in this country,” she said. “The King lives in your country, he’s from your country. He can’t be our King.”
She said “wasn’t fussed” if some people think she abused her power, as she has “the support of Aboriginal people around this country”.
Ms Thorpe said her outburst was for “global truth telling about the royals who caused so much devastation – to not only your people in this country but indigenous people around the world”.
The senator was also one of about 20 people protesting as the royals laid a wreath at a Canberra war memorial earlier on Monday.
She also refused to take an oath of allegiance to the late Queen when she became a politician.