The Northern Land Council has updated arrangements for recreational fishers wanting to access waters overlying Aboriginal land, with the changes coming into effect 1 January 2023.

On Thursday the Council resolved that current arrangements will cease at the end of this year and be replaced by a permit system. The permit system will be based on location, date and time and will initially be free of charge.

It will be available on the Northern Land Council website, which will be updated to reflect these arrangements before the end of 2022.

Council chairman Dr Samuel Bush-Blanasi said the updated arrangements represent "the start of a new era".

"Fourteen years after the High Court's Blue Mud Bay decision we are finally seeing the rights of Traditional Owners being respected. We will keep looking at the arrangements to make sure they reflect the legal rights and interests of the Traditional Owners of that country."

Dr Bush-Blanasi said the updated arrangements will balance the rights of Traditional Owners and the interests of recreational fishers.

"For the last two years the NLC has provided recreational fishers with a simple registration system giving recreational fishing access free of charge to the majority of Aboriginal sea country. There have been thousands of registrations during that time," Dr Bush-Blanasi said.

Permit-free fishing will continue for popular fishing areas around Darwin and Bynoe Harbours.

Long-term permit-free access arrangements will also continue to apply in the Daly River, Nhulunbuy, Port Keats and McArthur River regions, based on existing agreements between the Northern Territory government, the Northern Land Council and Traditional Owners.

The parts of the Finniss River and Mini Mini areas that are closed to recreational fishers under the current system will remain under the new system.

The Northern Land Council is currently working with the Territory government to progress negotiations with Traditional Owners for long-term agreements for recreational fishing in these areas.

NLC chief executive Joe Martin-Jard said the Council has a positive working relationship with both the commercial and fishing tourism sectors.

"Commercial operators have been advised that Section 19 agreements under the Land Rights Act will be required to operate on waters overlying Aboriginal land from 1 January 2023. The NLC will continue to work in good faith with Traditional Owners and all other stakeholders," said Mr Martin-Jard.

The permit system will be accessible on the Northern Land Council website before the end of the year.