Australia’s largest native title settlement is facing a second legal challenge from a group of traditional owners who say the process was unfair and did not represent the will of all 35,000 Noongar people.

The $1.3bn agreement was signed between the South West Aboriginal Land and Sea Council, which formally represents Noongar native title holders, and the Western Australian government in 2015.

It was ruled invalid by the federal court in 2017 after a successful challenge from a group of traditional owners who voted against the deal and said they did not consent to the signing of an Indigenous land use agreement.

The six ILUAs making up the Noongar agreements were approved by a majority of voters at six authorisation meetings, but the margin for one of the deals was just four votes.

The court ruled that an ILUA was only valid if it had the consent of every registered native title holder, rather than just a majority. That prompted the federal government to hastily rewrite the Native Title Act to protect dozens of other ILUAs, including a disputed agreement over the Adani coalmine, from also being overturned.

The agreements were registered with the national native title tribunal last month, after the native title registrar conducted a 12-month review and ruled that the authorisation process had been conducted correctly.

But some Noongar traditional owners disagree and have lodged an application for a judicial review.

Among them is Naomi Smith, a Minang and Goreng Noongar woman who said the decision to authorise the ILUA was not reflective of the wishes of the broader Noongar population, most of whom did not take part in or vote on the native title process.

Smith said less than 5% of the Noongar population had voted in the authorisation process and those who had were not properly informed of the risks of signing the deal. The process also did not allow for people who were in custody to vote.

The agreement covers 200,000 sq km stretching from north of Perth down to Albany on the south coast, and including areas of coastline and sea.

The ILUA extinguishes native title over the settlement area in exchange for a benefits package which includes depositing $50m a year over 12 years into the Noongar Boodja perpetual trust and transferring 320,000 hectares of freehold and leasehold land to that trust, to be developed and used by the Noongar community.

“It is not about money, it is about the land, and saving our land from mining,” Smith said. “If this deal goes through, the south-west will not be worth living in.”

Smith was one of four traditional owners behind the first federal court challenge, alongside Mingli Wanjurri McGlade, Margaret Culbong and Mervyn Eades. The same group, with Fabian Yarran replacing Eades, have initiated the second challenge.

The South West Aboriginal Land and Sea Council chair, Jeanice Krakouer, said the council continued to represent the majority of Noongar people.

“We respect the right of aggrieved people to appeal the registrar’s decision, but we will continue to act on the instructions of the majority of Noongar people who voted to accept and implement this agreement,” Krakouer said. “Our focus is on bringing the Noongar people together in healing and ensuring that we build a solid future for generations to come.”

Smith said she was “quietly confident” the legal challenge would succeed, but said even if it was it could be overruled again by federal parliament.

WA’s Aboriginal affairs minister, Ben Wyatt, said he was “very keen to see the settlement commence as soon as possible.”

“The Noongar people have been waiting a long time to see this process finalised,” he said. “However, objectors have a right to have their objections heard and dealt with by the federal court, and it is only appropriate to await the court’s judgment.”