Eight Quandamooka Elders have lodged a Federal Court application to stop the controversial whale centre development on North Stradbroke Island.
The protest, which has lasted more than three years, will now take a legal route.
Earlier this year the Quandamooka Truth Embassy set up tents at the Point Lookout headland in a last ditch effort to stop the centre being built on the site.
Protesters say the headland is a sacred site and the development poses a significant risk to cultural heritage and the environment.
The centre received planning approval in March 2020, and is set to feature a 15-metre skeleton of a humpback whale which washed ashore in 2011.
The state government awarded a building contract earlier this year, and construction was due to start in February. However, the tent embassy has delayed construction on the site.
A petition to prevent the development has attracted more than 55,000 signatures.
The legal team representing the Quandamooka Elders has called for federal Environment Minister Sussan Ley to make an emergency declaration to protect the area.
A Quandamooka Truth Embassy spokesperson said the minister's declaration would mean a step closer to long term, permanent protection of the area.
Earlier this year, Ms Ley made a declaration to protect the sacred Wiradjuri women's site from the development of a go-kart track at Mount Panorama.
The Quandamooka Yoolooburrabee Aboriginal Corporation is working with the Environment Department on the whale centre development.
A Environment Department spokesperson confirmed they had received applications under section 9 and 10 of the Aboriginal and Torres Strait Islander Heritage Protection Act 1984 on behalf of the Elders.
"The department is currently considering both applications," he said.
Section 9 provides for a short-term emergency protection declaration over an area that is under serious and immediate threat of injury or desecration.
Section 10 provides for a long-term declaration over a specified area that is under threat of injury or desecration.
