Fortune Agribusiness plans to build a 3500-hectare irrigated fruit and vegetable farm at Singleton cattle station, about 380 kilometres north of Alice Springs.

It was awarded a licence to extract 40 billion litres of underground water annually for 30 years, causing concern among Indigenous groups and environmentalists.

It triggered an independent review of the licence, with the panel finding the decision to grant it was largely correct.

However, the review has suggested some additional licensing conditions.

This means the original water extraction licence has been cancelled and a new substituted licence has been supplied detailing "improved and additional conditions".

These include a detailed assessment of the water resources on Singleton Station and a cultural values impact assessment.

Fortune will also need to demonstrate that its project will not result in an unacceptable impact on water-dependent cultural values.

The NT Environment Centre has questioned the licence review process, saying its in disbelief over the decision.

"We're extremely troubled by the NT environment minster's last minute decision to handball this review to the Minister for Territory Families," director Kirst Howey told AAP.

"There's no way Minister Worden had time to digest and understand the complexity of the information required to understand this project and its impact."

Ms Howey said the Fortune project's proposed water extraction could irreversibly damage ecosystems and cultural sites.

It may also cause the aquifier the water will be pumped from to drop by 50 metres, according to a hydrology study.

"This is not sustainable on any measure," she said.

The Central Land Council says the NT government is putting profits before water rights. It will explore other legal avenues to challenge the latest decision.

"We are alarmed and appalled at the lack of procedural fairness," chief executive Les Turner said.

"The government can only rebuild trust if it scraps the licence and starts from scratch, doing a full public assessment of the potential impacts, as its own review panel proposed.

"The licence is simply too big, too risky and threatens our sacred sites."

Mr Turner said the decision hands responsibility to protect important Aboriginal cultural sites to Fortune Agribusiness.

The Fortune project plans to cultivate permanent crops such as mandarins, grapes and avocados with potential annual production revenue of $180 million.

About 110 full-time jobs and 1350 seasonal jobs are expected to be on offer along with opportunities for businesses in nearby towns, such as Tennant Creek.

The groundwater is expected to be released to Fortune in four stages over the next decade, peaking at 40,000 megalitres through about 100 bores.

Fortune Agribusiness and the NT Farmers Association declined to comment.

Australian Associated Press