The Aboriginal Areas Protection Authority Board has raised concerns, with one Board member quitting, over adding SHDarwin Hotel and the Darwin Waterfront Corporation as recorded parties to the 2004 Authority Certificate issued for the Waterfront re-development under a new law which compels AAPA to process such applications without further consultation.

On Thursday, AAPA noted in a statement that Authority Certificates are based on "consultation with Aboriginal custodians" and set out the conditions for carrying out specific works on an area of land or water near sacred sites. The Certificate for the Waterfront re-development was issued to the NT Government more than 20 years ago.

However, the Waterfront application marks the first use of the NT Government's recent amendment to the Sacred Sites Act which allows additional parties to be added to an existing Authority Certificate and requires the Authority to process such applications without further consultation.

The AAPA Board said on Thursday that "due to this issue, AAPA Board Member Rachel Perkins resigned effective immediately".

Mr Bobby Nunggumajbarr, Chair of the Authority Board, said the Authority supports responsible development across the Northern Territory, but has "very serious concerns" about the Waterfront situation.

"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."

Mr Nunggumajbarr said more recent Certificates for development around Stokes Hill, including for the Larrakia Cultural Centre, set strict height limits to protect the sacred site.

"Larrakia custodians have been very clear that the current SH Darwin Hotel design will impact the site," he said.

"This application has put the Board in a difficult position but under the amended Act we must add the recorded parties."

The AAPA Board said it will be writing to the Federal Minister for Indigenous Australians, Senator Malarndirri McCarthy, and the Federal Minister for Environment and Water, Senator Murray Watt in support of Larrakia custodians and their objections to this development.