The Federal Court has dismissed a legal challenge to a lease agreement between Aboriginal traditional land owners in the Northern Territory and mining giant Rio Tinto.

In 2011, the Federal Government approved a 42-year lease agreement over land used for the Gove alumina refinery near Nhulunbuy in East Arnhem Land.

Aboriginal leader Djiniyini Gondarra estimated the deal was worth $19 million a year to Aboriginal clan groups in the area.

He said some groups were missing out on receiving any money.

Dr Gondarra started legal action on behalf of the Dhurili nation, arguing that the lease and agreement were invalid because the Northern Land Council (NLC) had failed to properly consult and advise all relevant clans.

At one point, Dr Gondarra suggested the Dhurili nation were traditional owners of part of the leased land but that was disputed and there was no contrary evidence tendered.

In her judgement, handed down in Melbourne yesterday, Justice Susan Kenny dismissed the challenge, ruling that the then Federal Indigenous Affairs Minister Jenny Macklin had fulfilled her obligations in approving the agreement.

Rio Tinto will close the alumina refinery later this year but will continue mining operations.

Traditional owners will continue to earn royalties from the bauxite mine.