Footage has emerged that allegedly shows commercial barramundi gill-nets strung across wide stretches of remote Northern Territory waters where commercial fishing is banned.

Traditional owners and charter fishing operators from the Arnhem Bay area have been left outraged by the alleged discovery, branding the commercial operators as "disrespectful" and "a disgrace".

The Aboriginal landowners own rights to the sea up to the intertidal mark, and last year banned commercial fishing in their waters in both Arnhem and Buckingham Bay after allegations of environmental destruction and overfishing by the commercial operators.

The footage, shot by a charter fishing operator in the Arnhem Bay area, shows dead fish caught in the gill-nets, which traditional owners believe could be in shallow waters within the intertidal zone.

Mulka MLA Yiŋgiya Guyula alleged that, in this most recent instance, the commercial fishers were "killing a lot of fish and doing a lot of damage without our consent".

"It is a disgrace, it is disgraceful, there is no accountability and no oversight," he said.

"Rangers don't have the resources to go out and investigate what's going on in the rivers, and whether it's been done safely or not, and we are very, very sure the fishermen have been disrespecting [traditional owners' wishes]."

Kane Dysart, the executive officer of the NT Guided Fishing Industry Association, said he'd had reports from operators that the commercial fishers were "setting their nets right on the closure boundary recently implemented by traditional owners".

"They're really walking a fine line between what is legal and what isn't," he said.

"[But] it's disrespectful and directly contravenes what traditional owners are trying to do in that area."

NT Recreational Fisheries Minister Joel Bowden said the government would investigate what he described as the "very, very serious" allegations.

In a statement, the NT Seafood Council denied commercial fishing vessels had been into the banned areas in Arnhem Bay, but acknowledged they had been operating beyond the restricted area.

Council chairwoman Joanne Butterworth-Gray said NT fishing authorities were "informed in advance of all operations in the Arnhem and Buckingham Bay areas, ensuring transparency and security in our processes".

"Commercial operators are dedicated to forming long-term access agreements with traditional owners," Ms Butterworth-Gray said.

The NT's recreational and charter fishing industries have for months been calling for the controversial practice of gill-netting to be phased out, as has been done in Queensland.

Arian Pearson grew up fishing the waters of his mother's homeland Rorruwuy, a Datiwuy clan outstation that shares the waters of Arnhem Bay with other Yolŋu clan groups.

"There are very significant sites, sacred sites where there are turtle sites, food sites, and other areas that are very significant as well," Mr Pearson said.

He said he'd seen numerous instances over the years of dead sea-life washing up on Yolŋu shores from gill-netting, and called for formal agreements to be made between fishers, traditional owners and rangers, for commercial operations to continue in the region.

"There needs to be more information given to the public and to ranger groups as well, who are looking after the country," he said.

"We need to start looking at more sustainable ways to fish, and to share that responsibility of looking after the country [and] those protected areas in general."

The NT government has been reviewing practices in the barramundi fishing industry, with Mr Bowden confirming that he would have "more to say on that" prior to the NT election in August.