The prime minister has refused to provide any assurances the country's peak body for indigenous survivors of domestic violence will have its funding extended.
But the responsible government agency says allocated money will increase in a restructure of the groups.
Funding for the National Family Violence Prevention and Legal Services Forum, which represents 13 frontline organisations, is due to expire in June 2020.
The forum supports and advocates on behalf of 13 organisations that work with Aboriginal and Torres Strait Islander survivors of family violence.
Chair Antoinette Braybrook said the limited resources available to the group would now be drained by a fight for funding.
"It rips Aboriginal and Torres Strait Islander women's voices out of critical national conversations," she said.
Prominent campaigner Rosie Batty said the decision sent the wrong message about eradicating family violence.
"The voices of women and children have never needed to be heard more than now," she said.
Scott Morrison was questioned about the decision in Canberra on Friday.
"There are always issues of ongoing funding right across the budget," he told reporters.
"There will be a budget for 2020-21 and we will consider all these matters in the normal way."
But the National Indigenous Australians Agency insisted the funding will continue, just in a different form.
"Consistent with the findings of an independent evaluation, the government advised the National FVPLS Secretariat of a change to its current funding arrangements to improve services," a spokesperson said.
"Current funding arrangements for the National FVPLS Secretariat will cease on June 30, 2020."
The agency said funding for providers had increased by $3 million to $75 million over the three years starting on July 1 next year.
Australian Associated Press