The Northern Territory Government says it is seeking advice on how it can run a crocodile safari hunting trial without Commonwealth approval.

There have been angry reactions to a decision by Federal Environment Minister Greg Hunt to prevent crocodile hunts in the Top End.

The Territory wanted Federal Government approval for 50 crocodiles to be taken by fee-paying safari hunters as part of a one-year trial.

In knocking back the proposal Mr Hunt said there was a risk of cruel and inhumane treatment.

Territory Land Resource Management Minister Willem Westra Van Holthe says safari hunting would have provided economic development opportunities for remote Indigenous communities.

"What we need to point out here is that Territorians best know how to manage the crocodiles up here in the Northern Territory," he said.

"I would point out that I don't think Greg Hunt has any idea how to manage crocodiles in an area that he has little idea about.

"I am sure if he had crocodiles in his swimming pool or his back yard, he would want them managed."

About 500 crocodiles are killed each year in the Territory as part of a management plan.

The Northern Land Council (NLC) says federal politicians should be open to unorthodox business ideas such as crocodile safari hunting that could create economic opportunities in remote parts of the Territory.

NLC chief executive officer Joe Morrison says there should have been more consultation with traditional owners about the proposal's benefits, and how it could have been done humanely.

"Instead of just saying no to these things there needs to be a bit of consideration of what is really going on up here, and what are the opportunities presenting themselves for Aboriginal people to get into these niche industries," he said.