The free online permits grant access to fishing spots across about 2000 kilometres of Indigenous sea country, the Northern Land Council says.

"The NLC has statutory responsibilities to assist traditional owners to manage their country and we take those responsibilities very seriously," chief executive Marion Scrymgour said.

Known as the Blue Mud Bay registration process, the new requirements start on Monday, with free access until December 31, 2022.

Talks about what happens after that are ongoing.

The NLC says the new system reflects the 2008 High Court of Australia decision that recognises Aboriginal ownership of tidal Aboriginal land - sometimes called the "intertidal zone" - in the Northern Territory.

Consultation with traditional owners for access to the popular Finniss River and Mini Mini systems has not been finalised.

NT Minister for Parks and Rangers Selena Uibo said the government was focused on ensuring long term access for recreational fishers.

"We believe we are firmly on the right path to providing some resolutions in the long run about access arrangements," she said.

The new registration system follows agreements permitting amateur access to fishing areas along 1,100km of other Indigenous sea areas, that have been in place since 2013.

The Amateur Fishermen's Association of the Northern Territory has called on the government to act in the interest of all Territorians, saying fishers are locked out of some of the most popular and socially significant recreational fishing areas in the Top End.

"While we fully respect traditional owners' rights to decide upon access to their waters, AFANT is not convinced that the new regime is anywhere near the best solution to resolve Blue Mud Bay access," a spokesman said in a statement.

"Instead, it is a product of an unbalanced deal, and seems like a failure by the NT government to secure the best possible outcome in the interest of all Territorians."

A regulatory framework via the NT Fisheries Act and Land Rights Agreements already exists for professional fishers and guided fishing tour operators.

The intertidal zone is the area between the high tide and low tide water marks.

Fishing spots that are currently only accessible by vehicle may also require an NLC transit permit.

The Northern Territory coastline is about 5400km in length.

Anglers can still access many popular NT fishing spots not covered by the agreement without registering, including Darwin Harbour, the Adelaide River and the bottom half of the Tiwi Islands.

Australian Associated Press