Assistant Minister for Indigenous Australians Malarndirri McCarthy moved a motion to display the flag on Wednesday's sitting and it was passed on the voices.

The flags will be displayed within the next three weeks.

But while the motion was moved and passed with no speeches, it caused controversy earlier in the day when Senator Hanson angrily left the chamber during the opening acknowledgement of country.

President Sue Lines acknowledged the Ngunnawal and Ngambri people as traditional custodians of the Canberra area and paid respect to elders past and present at the opening of Wednesday's sitting.

Senator Hanson interjected, yelling: "No, I won't and never will", before exiting the chamber.

The One Nation senator told AAP she could not accept the welcome to country or the motion to raise the Aboriginal and Torres Strait Islander flags in the Senate chamber.

"I've been feeling this way for a long time," she said.

"I have called from the first day for equality for all Australians. I see this as divisive."

She said if anyone needed acknowledgement it was "our people that have fought for this country. People who have sacrificed their lives".

Senator Hanson added the flag had "never been voted on" and criticised the acknowledgement of country.

"No Australian or government-appointed panel had any chance to comment on the design, and no Australian has ever had the opportunity to vote to approve the Aboriginal flag," she later told the Senate.

"It's not for senators to decide whether the Aboriginal and Torres Strait Islander flags are flown in this chamber.

"I suggest that (we) actually allow the people of Australia to vote whether they want those flags flown."

Indigenous Greens senator Lidia Thorpe criticised Senator Hanson on Twitter, calling the action "disrespectful".

"Day two of the 47th parliament and racism has reared its ugly head," she wrote.

"Pauline Hanson disrespectfully stormed out of the acknowledgement of country in the Senate, refusing to acknowledge 'those people'.

"You want to make parliament safe? Get rid of racism."

Labor senator Jenny McAllister says the acknowledgement of country is "a courtesy ... that brings people together".

"Everyone has to make their own decision about how they behave in this place and what they bring to this place. It's up to Pauline Hanson to make her own decisions about," she told the ABC.

"But I am really clear about my position. Acknowledging country and acknowledging traditional owners is the right thing to do."

The lower house on Wednesday agreed to set up the first dedicated joint standing committee on Aboriginal and Torres Strait Islander affairs.

The two parliamentary chambers have a record 11 Indigenous MPs and senators.

Australian Associated Press