Host David Koch quickly threw to an ad break, but later in the show about 50 protesters formed a group in shot, behind Koch and co-host Samantha Armytage, forcing the pair to acknowledge the disruption.
The hosts repeatedly said the protest was not related to a controversial segment on Indigenous adoption aired last month.
"As you can see, we're being joined by some Aboriginal protesters who are protesting throughout the Commonwealth Games. They are protesting land rights and genocide, being quite noisy," Koch said.
"Some of the language leaves a lot to be desired. We are trying to block out some of the more angry, nasty and vile bits of this.
"We respect people's right to protest."
However, the protestors were also chanting "Shame Sunrise, shame" and called for Armytage to apologise or be sacked for the March segment in which she and two panellists discussed Aboriginal adoption.
Last month, hundreds of people gathered in Sydney's Martin Place, where the show is normally recorded, labelling the segment racist.
On Tuesday, about a dozen police lined up between the beach-side stage and the protestors, though no arrests were made.
Indigenous protesters also disrupted the final day of the Queen's Baton Relay and also gathered outside Carrara Stadium before the opening ceremony of the Gold Coast Games, resulting in three people being arrested and charged with public nuisance.