The Murray-Darling Basin Authority has criticised South Australia's royal commission into the basin, branding a key recommendation "reckless".
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The commission's contention that the basin plan should be effectively abandoned would set back progress towards a healthy river system, the authority said.
The MDBA said the basin plan was starting to deliver and once fully implemented would reduce water extractions by around 20 per cent and improve water use efficiency.
"The authority was established to develop, implement and monitor a basin plan for the sustainable management of the basin's water resources," it said in a statement on Wednesday.
"While many people support the concept of a basin plan, there is often sharp disagreement up and down the rivers, and across different stakeholder groups, about the most appropriate settings."
In his inquiry, commissioner Bret Walker also ruled that the basin authority acted unlawfully, committed gross maladministration and took a "head in the sand approach" to climate change.
His final report found river allocations were driven by politics rather than science and called for a complete overhaul of the Murray-Darling Basin Plan, calling for a scientific approach to determining the return of water to the environment.
The authority rejected claims of maladministration and said it demanded the highest standards from its staff and board members.
It said it was also committed to always using the best available science and conducting its work transparently.
"As with any science-based organisation we can always do more to improve our work and our transparency and we are committed to taking on the challenge," the authority said.
However, it agreed with the concerns of the royal commission over the slow progress in recovering an extra 450 gigalitres of water for environmental flows through efficiency measures.
"More work is needed to protect environmental flows," the authority said.
Australian Associated Press
