Environment Minister Sussan Ley has since reconsidered the matter in light of the ruling, and informed proponent Wild Drake Pty Ltd of her decision on Thursday.

The court had found that the original decision by former environment minister Melissa Price that no approval was required had been flawed.

Ms Ley has now decided that the proposal be assessed as a Controlled Action under the Environment Protection and Biodiversity Conservation Act.

She said the matter had attracted "considerable public complaint and legal challenge".

"While acknowledging the Department's 2018 determination (accepting submissions from Wild Drake Pty Ltd that this was not a controlled action) and its current advice, I have determined that the likely impacts to the unique values of the Tasmanian Wilderness World Heritage Area warrant a formal assessment," Ms Ley said.

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"This decision does not pre-determine an outcome, but it does ensure a detailed assessment is made and all possible impacts on the TWWHA are considered.

"Under both the current EPBC Act and under our proposed streamlining of approval processes, the Commonwealth maintains, as a signatory to the UNESCO World Heritage Convention, responsibility for ensuring the protection of World Heritage Values, just as it will ensure that binding national standards underpin environmental decisions in the future."

In a statement, Wild Drake co-owner Daniel Hackett said the decision to carry out another assessment was a surprising outcome.

"It is our understanding that this further assessment will occur off the preliminary (current) documentation, over the period of the next fortnight, followed by a further public comment period," he said.

"The decision comes as a surprise, as we are aware that the current departmental recommendation, along with a previous Federal Court ruling, indicated that the project should be considered Not a Controlled Action, if conducted in a particular manner.

"Whilst surprised, we respect the decision of the Minister and will continue to do as we have done all along, which is adhere to the assessment processes, and ensure that Australia's highest environmental benchmarks are achieved."

The proposal has faced vigorous opposition from environment groups, bush walkers and fly fishers over its use of a helicopter to fly visitors to an exposed rock landing area near Lake Malbena, and the plan to use a wilderness island for a private tourism development.

It was knocked back by the Southern Midlands Council, but approved on appeal in the Resource Management and Planning Appeal Tribunal.

It also faced an appeal in the Federal Court in relation to the environment minister's decision that it was not a Controlled Action, which succeeded on two grounds. Ms Ley's decision on Thursday was in response to this appeal.

Wilderness Society Tasmania campaign manager Tom Allen said the decision presented another opportunity for opponents to put their case to the Environment Minister as part of the public consultation process.

"This is not just an opportunity to present evidence, but also a huge opportunity for the public to have a say, and we know that people will have less of a say on planning matters in Tasmania in the future which is why this is so important," he said.

"We'll be encouraging people to put in their submissions. At the end of the day this is public land that could be privatised."