A vote to amend the constitution of the peak body for Indigenous community-controlled health organisations has been defeated.

It comes after criticism from the Queensland Aboriginal and Islander Health Council, who expressed "serious concerns" about the National Aboriginal Community Controlled Health Organisation's (NACCHO) conduct ahead of its AGM and Extraordinary General Meeting (EGM) in Canberra, on Ngunnawal and Ngambri Country.

QAIHC's concerns focused on the proposed changes to NACCHO's constitution, arguing they could "undermine NACCHO's transparency, accountability, and community-controlled ethos".

They urged all NACCHO members to consider the ramifications of the changes.

Chairman Matthew Cooke said as the peak organisation representing the sector, NACCHO needed to be "fair and transparent," arguing they needed to be about community-control, "not controlling communities".

QAIHC said NACCHO were "positioning" themselves to take on a "significant role" in holding and commissioning funds, which Mr Cooke said could lead to a conflict of interest.

"If NACCHO is to have a significant funds-holding and commissioning role, as it is clearly seeking to do, it must be a transparent and accountable organisation," Mr Cooke said.

On Tuesday afternoon, National Indigenous Times was made aware the vote had not passed.

Mr Cooke said NACCHO needed to "recognise" it couldn't be both an effective peak body, and a funds holder.

"These roles are incompatible," he said.

"NACCHO can either advocate with neither fear nor favour for the sector and First Nations peoples, or it can hold and allocate funds—it can't do both."

He argued accountability was something everyone demanded of governments and needed to be replicated in Indigenous organisations.

He added in the wake of the failed Voice referendum, which was rife with dis- and misinformation, contemplating amendments that will make NACCHO a "less transparent or accountable organisation," was "madness".

On Tuesday morning, QAIHC released a statement saying they were concerned with NACCHO's conduct, with Mr Cooke arguing he had his reservation to the AGM declined by NACCHO, through their Company Secretary.

Mr Cooke said it was an "extraordinary step," with the current constitution "affording me a clear right to register and attend as a Member Delegate".

"For NACCHO, the national peak body for our sector, to deny one of its members a voice, and our right to self-determination, in such an important conversation, despite it having no basis in its constitution, to do so is extraordinary and unprecedented," he said.

NACCHO refuted the claims made by Mr Cooke, telling National Indigenous Times his statement was "factually incorrect".

"Delegates were required to register to vote 48 hours prior to the AGM and EGM, and Mr. Cooke did not complete this process," a NACCHO spokesperson said.

"He was permitted to attend the meeting but chose to leave."

Member organisations are entitled to have two voting representatives at the AGM and must provide at least 48 hours' notice of attendance to NACCHO prior to the date of the AGM, a letter from Company Secretary, Erin McMullen, says.