Indigenous traditional owners in remote West Arnhem Land have lost patience with being prohibited from selling valuable barramundi from their coastal waters, while commercial trawlers do just that.

Forty-two clan groups are threatening a three-year ban for commercial barramundi boats in coastal waters between Cape Stewart and Braithwaite Point if the Northern Territory Government and Northern Land Council (NLC) can't agree on a deal about the conditions for access to Indigenous Territory coastal waters.

The Arnhem Land traditional owners had hoped that after the 2008 Blue Mud Bay High Court decision, which returned 80 per cent of the Territory coastal waters to Indigenous people, they would get control of their sea country.