The Central Land Council says the federal government must intervene in Aboriginal heritage protection in the Northern Territory for the first time since the 1990s, when a Labor minister stopped a sacred Arrernte women's site from being destroyed.

The call comes after Larrakia Traditional Owners raised alarm at a decision forcing the Aboriginal Areas Protection Authority (AAPA) Board to approve a development application for the Darwin waterfront.

The application, lodged by the NT Government, adds the Darwin Waterfront Corporation and SH Darwin Hotel Pty Ltd as recorded parties to Authority Certificate C2004/004, which covers the waterfront precinct.

CLC chair, Warren Williams, said he supported Larrakia custodians trying to protect their sacred site as well as the independence of the AAPA.

On Thursday, AAPA said in a statement Authority Certificates are based on "consultation with Aboriginal custodians" and set out conditions for carrying out work on land or water near sacred sites. The Certificate for the Waterfront redevelopment was issued to the NT Government more than 20 years ago.

But the new application marks the first use of recent amendments to the Sacred Sites Act, which allow additional parties to be added to existing certificates and require the Authority to process applications without further consultation.

Mr Williams argued the AAPA being forced to approve the insertion of two new parties in a 20-year-old sacred site clearance certificate without Traditional Owner consultation demonstrated why the CLC fought against changes to the act.

"This is the first test of the controversial changes and it fails the traditional owners, just as we predicted," Mr Williams said.

"My heart goes out to the Traditional Owners. We will stand with them in their fight for their right to protect their sacred site."

CLC chief executive, Les Turner, pointed to the actions of former Aboriginal Affairs Minister Robert Tickner, who in 1992 used federal heritage laws to block the NT Government from building a $20 million flood mitigation dam near Alice Springs, which would have destroyed a sacred women's site.

The decision was welcomed by Community and condemned by the Country Liberal Party (CLP) government at the time, with Chief Minister Marshall Perron accusing the federal government of acting like 'big brother'.

Mr Turner said the current CLP government had shown why "it can never be trusted" to protect sacred sites and called for Commonwealth intervention.

"The federal government should clarify the power of the NT government to make laws to protect our sacred sites and work with our land councils and traditional owners to strengthen heritage protections," he said.

This week, AAPA board member Rachel Perkins resigned "effective immediately" over the decision. The Board said it would write to Indigenous Australians Minister Malarndirri McCarthy and Environment Minister Murray Watt to back Larrakia objections to the development.

In praising Ms Perkins for "taking a principled stand," Mr Williams said the changes mean the AAPA is effectively an instrument of the CLP government and echoed the "concerns of the remaining AAPA members who find themselves in an impossible position".

He said he had also written to NT Minister for Lands, Planning and Environment Josh Burgoyne.

"You told our council that AAPA certificates could be transferred only if companies are 'doing the exact same work,'" Mr Williams wrote.

The CLC said Mr Burgoyne had written to them in May and confirmed certificates could be transferred or have additional parties added, "as long as the proposed work and use of the land are the same".

In his letter, Mr Williams accused the minister of ignoring concerns and failing to fix the law to address them.

"You did not make sure the protections you promised were included in the final legislation," he wrote. "You have placed our sacred sites and our culture at risk."

The Larrakia Nation Aboriginal Corporation also voiced its opposition, warning the decision undermined both fairness and cultural protection.

"The recent legislative amendments require the AAPA Board to process such applications without meaningful consultation with custodians, undermining both procedural fairness and the integrity of the Authority's decision-making," it said in a statement.

"Legislative and ministerial overreach has stripped AAPA of its role as an independent statutory authority, reducing its functions to that of administrative endorsement rather than cultural site protection.

"The original Waterfront Authority Certificate did not contemplate or provide for the construction of a high-rise hotel adjoining the Convention Centre and proximate to a registered sacred site."

AAPA chair Bobby Nunggumajbarr said the Authority supported responsible development but was concerned about the Darwin project.

"Sacred sites and development often co-exist and the Darwin Waterfront precinct is proof of that. The precinct demonstrates that with proper consultation and respect, development can proceed in a way that benefits all Territorians, whilst also protecting the cultural heritage of the Larrakia people," he said.

"However, the Board has very serious concerns about the use of a 20-year-old Certificate to progress the SH Darwin Hotel proposed hotel project.

"The old Waterfront Certificate does not detail a high-rise hotel next to the Convention Centre or alongside the registered sacred site. Plans for a tower in that location were not part of the original Larrakia consultation."

This article was updated on Saturday, 27 September, after the CLC recalled and clarified a press release.