Three Indigenous senators moved a motion to coincide with NAIDOC Week to have the flags hoisted on the floor of the upper house.

Labor's Malarndirri McCarthy and Pat Dodson, along with Greens senator Lidia Thorpe wanted them raised alongside the Australian flag.

But coalition senators opposed the move, narrowly defeating the motion 29 to 28 votes.

Cabinet minister Anne Ruston said there were many other circumstances to fly the Aboriginal and Torres Strait Islander flags.

"The government believes the Australian national flag, which represents all Australians, is the only appropriate flag to be flown in the Senate chamber," she told parliament.

The coalition then denied Senator McCarthy a chance to make a short statement on the issue, angering Labor frontbencher Murray Watt.

"This is NAIDOC Week. To deny a First Nations senator leave to speak for one minute on this motion is I think something the government will regret," he said.

The government then relented, allowing Senator McCarthy and Senator Thorpe a chance to speak.

"Thank you so very much for allowing black people to speak about the black flag," Senator Thorpe said.

Senator McCarthy said NAIDOC Week was a chance to show Australia politicians could unite the country.

"The Aboriginal and Torres Strait Islander flags are also national flags," she said.

Senator Thorpe said she wasn't sure where other senators had come from, but her people had been in Australia for thousands of generations.

"Can I remind you all that we are on stolen land? The Aboriginal flag represents the oldest continuing living culture in the world," she said.

"The Aboriginal flag is what we identify with, what we connect with, just as you connect with the colonial flag that you love and you appeal to."

Australian Associated Press