Federal Water Minister Tanya Plibersek may not have read the NSW Fractured Rock Water Resource Plan before accrediting it, the federal court has heard.

Murray Lower Darling Rivers Indigenous Nations (MLDRIN) took legal action over the plan, appearing in court earlier this week, over allegations Indigenous communities were either not adequately consulted or not consulted at all on the plan.

MLDRIN, a Confederation of First Nations from the southern half of the Murray-Darling Basin, said on Thursday that the Minister had "conceded that she made a mistake" in accrediting the plan.

The group notes that the minister was required by law to read the plan prior to accrediting it.

"The Minister has now admitted that she did not have a copy of the Plan before her when she accredited it, as required by s 63(5) of the Water Act," MLDRIN said in a statement.

The organisation's chair, Brendan Kennedy, said the Minister's failure to lawfully accredit the WRP has "led to First Nations feeling that our rights and interests are no more than a 'tick and flick' process just as they were under the previous Coalition government".

"The Minister was the key authority that could have listened to our concerns, but she did not. This left MLDRIN with no other option than to seek legal remedy. This legal case is really important to us as it brings to the forefront how the water management system disenfranchises and marginalises First Nations, through 'tick and flick' processes," he said.

A spokesperson for the federal Department of Climate Change, Energy, the Environment and Water told National Indigenous Times that "as a model litigant", the Commonwealth made a partial concession in relation to the Minister's accreditation decision, narrowing the issues to be determined at hearing.

"While the Minister had a range of material before her when making her decision, including the Murray-Darling Basin Authority's detailed assessment and recommendation and a brief of material prepared by the department, it could not be unequivocally established that the water resource plan was also before the Minister," they said.

MLDRIN deputy chair Grant Rigney said the legal challenge "highlights the need for a complete reset between the Federal Government approach to working with First Nations and their First Nations community controlled organisations".

"It's never been OK to adopt a 'tick and flick' approach with Nations, and we stand by our right to be treated as partners - not interest groups. We call on the Minister to take action today and stop the systemic 'tick and flick' approach applied to First Nations and their water interests, by her government and by the previous Coalition government," Mr Rigney said.

"It's time to invest in grass-roots Nations, and their organisations who desperately need to be resourced to participate equitably in the upcoming Basin Plan review in 2026 and the Water Act Review in 2027."

Other legal grounds argued at the hearing are questions around the extent and appropriateness of the consultation undertaken by NSW with First Nations about water resources in the area.

MLDRIN has asked the Court to find that the consultation that occurred with Nations was not enough to satisfy the requirements of the Basin Plan, such that the resulting recommendation of the MDBA that the Minister should accredit the Plan was invalid.

"We now await the Court's decision," the organisation said in a statement.

The Department spokesperson told National Indigenous Times that the "partial concession" regarding the Minister reading, or not reading, the plan "does not cover the Authority's recommendation to accredit the water resource plan, which the Commonwealth maintains is valid".

"The Federal Court will determine the validity of that recommendation. As no court orders have been made and the matter remains before the Federal Court, it would not be appropriate to comment further on the proceedings," they said.