Dozens of officers remain stationed outside and around the institution after protesters said they would "take Old Parliament House".
A video on social media shows people preparing for protests at a park in Canberra's city centre, with speeches being given to an audience of dozens.
"Did you notice how it was rainy ... and then the sun came out? It is because we are on the right side of history and doing God's work," one speaker told the crowd.
Police largely cleared the protesters' camp from the park opposite the now-museum on Friday, saying the group was illegally camping on Commonwealth land.
Hundreds of officers moved in to dismantle tents and personal belongings on the site, bundling them into a collection van.
There were tense standoffs between officers and protesters as items were removed and one person was charged with breaching bail conditions.
The Lore Not Law group - referring to Indigenous law typically passed by word of mouth - has been engaged in sustained protests, issuing the federal government "eviction notices" at Canberra landmarks including Old Parliament House and The Lodge.
Following the dismantling of tents, protesters moved to surround the nearby Aboriginal Tent Embassy and called embassy members "sellouts".
People at the tent embassy were seen yelling back at the group of protesters.
Embassy representatives have moved to distance themselves from the group of protesters, who they accuse of breeding a "cult-like mentality".
The police operation came following a court hearing for two men charged over a December 30 protest which saw the doors of Old Parliament House set on fire.
The fire has been linked to members of the protest group.
Bruce Shillingsworth Jr and Dylan Wilson were both granted bail after being charged with offences relating to the December 30 protests. Both men deny the charges.
Neither is allowed to enter the Canberra suburb of Parkes, where Old Parliament House is located.
Appearing in court on Friday, Shillingsworth - who the magistrate described as being a ringleader - said he was trying to disperse protesters, telling them not to go ahead.
Shillingsworth told the magistrate his first night in prison, following his arrest on Thursday and bail on Friday, gave him time to think.
He said he had planned to go down to the camp to defuse the situation and look at other avenues of peaceful protest.
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