The federal opposition has condemned the government's decision to scrap a dedicated day of Senate estimates hearings on Indigenous affairs, accusing Labor of having "slammed the door on accountability".

Senate estimates are one of the few opportunities for politicians to question ministers and senior public servants on government spending and performance.

Following the March federal budget, much of the estimates process was interrupted by the election campaign. The government added an extra sitting week to make up the time, but it did not restore a dedicated day for "cross-portfolio" issues, which often cover regional and Indigenous matters.

On Thursday, Liberal Senator Jonno Duniam said Labor and the Greens had voted to remove the separate day from October's hearings, calling the move "shameful".

"It is astounding that a Labor government that holds itself up as the champion of Indigenous Australians, in partnership with the Greens — who claim the same thing — would go and scrap a full day of hearings in the Senate estimates process relating to Indigenous matters," he said.

"It's not good for democracy, it is not good for accountability, and it's certainly not good for Indigenous Australians."

It is understood those topics will now be absorbed into other hearing days, but the opposition says it is the first time in 17 years that "cross-portfolio" matters will not have their own dedicated session.

Opposition spokesperson for Indigenous Australians, Kerrynne Liddle, argued the government was shutting the door on accountability. She said the estimates would have allowed the Coalition to prosecute the government on why four key Closing the Gap metrics "are going backwards".

"We also would have sought an answer to why Aboriginal communities in Central Australia are not feeling safer or optimistic for their future despite the Albanese Government throwing $300 million at its Better, Safer Future for Central Australia Plan," Senator Liddle said.

"The Coalition also holds significant concerns regarding the fact we can no longer ask ORIC what it is doing about the 1254 Indigenous organisations that failed to fulfil mandatory reporting requirements for the 2023/24 Financial Year."

Shadow Minister for Defence Industry and Defence Personnel, Senator Jacinta Nampijinpa Price, also criticised the government's decision, saying "Indigenous Australians deserve accountability for the billions spent in their name".

In a statement to National Indigenous Times on Friday, Senator Price argued that at a time when "outcomes are going backwards," both Labor and the Greens "are running from scrutiny".

"Youth suicide is up. Incarceration is up. Fewer children are starting school on time. These are shocking results, and instead of answering questions, Labor and the Greens have chosen to silence debate," the NT Senator said.

"The Albanese Government promised transparency. Yesterday, they proved they are more interested in hiding from scrutiny than delivering for Indigenous Australians."

Senator Duniam cited the Closing the Gap data as proof the government's policies are "failing Indigenous Australians" and said this warranted more scrutiny, not less. He added that politicians supporting the decision "should hang their heads in shame".

"How can you look at these [Closing the Gap] numbers and say what you've done today is good?" he asked.

A Coalition motion to overturn the changes was defeated on the floor.

In response, Labor's leader in the Senate, Penny Wong, said the opposition would still have opportunities to ask questions during other hearings and argued the Coalition "didn't oppose this change earlier in the day but now is feigning outrage".

"To the leadership of the Coalition in this chamber, for many years, I was the Senate leader in opposition," she said. "I remember it very clearly, and I consistently supported the government of the day in their parliamentary sitting pattern because that was the convention.

"It is unfortunate that the coalition wants to work with Senator [David] Pocock to change the parliamentary sitting, but that's a matter for them."

On Saturday morning, a government spokesperson told National Indigenous Times that the government had agreed to add three more days of estimates later this year to "allow for additional scrutiny."

"In this round of supplementary budget estimates, Indigenous issues will be a part of every day of estimates," the spokesperson said.

They added that closing the gap is a "whole of government responsibility," stressing it is the "responsibility of every Secretary and Minister to improve outcomes for First Nations Australians".

This article was amended on August 30 to include quotes from a federal government spokesperson.