Documents leaked to the Environment Centre NT show the Middle Arm project on Darwin Harbour would destroy 86 per cent of the endangered plant's remaining population.
The leaked assessment comes from the Northern Territory government's own draft environmental impact statement on the project.
The tiny herb, Typhonium sp. Cox Peninsula, was one of 35 plants and animals added to Australia's list of national threatened species in February.
The Environment Centre NT said the plant could go extinct due to land clearing on the Cox Peninsula if the proposed Middle Arm hub goes ahead.
The Middle Arm project would also harm critically endangered far eastern curlews and endangered black-footed tree rats, the environment centre said.
Typhonium species are seasonally dormant when conditions are dry and emerge from underground tubers during the wet season in Australia's Top End.
The federal government has promised $1.5 billion for dredging a river and building industrial jetties at the Middle Arm peninsula.
Environment Centre NT Executive Director Kirsty Howey said federal Environment Minister Murray Watt cannot approve a project that government scientists say is likely to drive a species to extinction.
"It's frankly immoral to proceed with a development that will destroy an endangered species' home almost in its entirety," she said.
The NT government's infrastructure department said the draft environmental impact statement had not been finalised or submitted and was expected to be released for public review and comment in 2027.
"It is premature to make judgements about potential impacts and how they might be managed until the assessments are finalised, particularly as the proposal gets refined," the department said.
It said the impact statement would describe commitments to avoid, mitigate or offset impacts to ensure the long-term protection of the environment.
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