Tensions boiled over amid wild scenes on Friday as protesters were moved on in Victoria Park, the planned site of the new stadium.
Several people were arrested including a man tackled to the ground by police in what critics described as a surprise raid.
Bulldozers are expected to begin clearing the way for construction of the $3.6 billion 2032 arena as early as Monday.Â
Magandjin Elders say they are "saddened that a situation that could have been managed through communication and respect instead became one of confrontation".
"We believe the heavy-handed response unnecessarily provoked protesters and created distress within the broader community," they said in a statement on Saturday.
"Victoria Park is a place of significance to many First Nations peoples and the concerns being raised by community members deserve to be heard with dignity and respect - not met with force and brutality."
Many had been camping in the park for months, with activists setting up a tent embassy.
Before this, authorities announced the site would be fenced off for five years from next week to build the 2032 Games centrepiece.
However, protesters appeared blindsided on Friday when police and Brisbane City Council asked them to move before imposing a 2pm deadline.
Protest organiser Derek Oram Sandy defiantly grabbed a microphone after the deadline and addressed the officers before eventually approaching them.
Officers and council workers responded by slowly approaching the tents, sparking arrests as the site was dismantled and property removed.
Five protesters were taken into custody, with one later released without charge.
"Our embassy has stood strong for more than seven weeks protecting one of Brisbane's most culturally significant sites from destruction and we are not going anywhere," Mr Sandy said.
"We have the right to be here. We are here to protect Country, culture and this sacred place for future generations."
Greens MP Michael Berkman watched as police surrounded the camp, accusing Brisbane Lord Mayor Adrian Schrinner of a "dodgy, underhanded approach".
"Everyone was anticipating Monday would be the day something would happen - it was a complete surprise," he told AAP.
The state government and council defended the decision to move against the protesters, saying their presence had become a safety issue with construction imminent.
Fences are being erected around the site, with ownership of the land to be transferred to the 2032 Games Independent Infrastructure and Coordination Authority.
Consultation with Traditional Owners will continue as the authority progresses delivery of the stadium.
The government has converted Victoria Park to freehold land but the project faces legal challenges under section 10 of the federal Aboriginal and Torres Strait Islander Heritage Protection Act.
Federal Environment Minister Murray Watt can halt proceedings but hasn't indicated when a decision on applications will be made.
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