Indigenous organisations are hoping for federal government funding later in the year to help close the gap.
The Closing the Gap agreement aims to end the divide between Indigenous and non-Indigenous Australians in social, economic and health areas, and now includes 16 targets after the original seven were overhauled because they were not on track to be met.
The Coalition of Peaks, which represents more than 50 Aboriginal and Torres Strait Islander organisations, did not expect funding for Closing the Gap in the budget.
The group's lead convener Pat Turner is encouraged by significant spending in aged care, Indigenous skills and jobs, mental health and women's safety.
"But this is very much a wait and see budget as the majority of funding directed towards Closing the Gap won't be announced until later in the year," she said.
"I'm pleased to see the funding laid out in this budget contains promising investments in crucial areas that affect our people.
"Our main concern with every commonwealth budget is how the funding will trickle down and benefit our people on the ground."
The latest Closing the Gap agreement was inked last July by all levels of government and the Coalition of Peaks.
The targets include closing the life expectancy gap between Indigenous and non-Indigenous Australians by 2031.
Last year's budget included $46.5 million to help Indigenous organisations tackle the targets, to help build their capacity and business models.
Labor's spokeswoman for Indigenous Australians Linda Burney believes Tuesday evening's budget should have had extra money for the targets.
"If we want to see real progress on this critical national effort, we need to see it backed by a genuine commitment and adequate funding from this government," she said on Wednesday.
Indigenous women's health and welfare organisation Waminda says the budget was a missed opportunity to work with Aboriginal health organisations to help women have choice and control in birthing.
"Birthing on country is not some pie in the sky concept - it is real, it is proven to work, and it will help Australia close the gap on mortality in First Nations children younger than five," Waminda chief Faye Worner said.
"The rate of Indigenous infant health issues and infant deaths in Australia is shameful, but without investment from the federal government, we cannot seriously make inroads to close the gap in infant mortality rates."
In 2018, the Indigenous child mortality rate was twice that of non-Indigenous children.
"What we were hoping to see was a commitment to capital funding for an Australian-first birthing on country and community hub," Ms Worner said.
Australian Associated Press