AUSTRALIA'S premier scientific organisation says the Murray Darling Basin Authority has misinterpreted and misrepresented its data.

CSIRO has written an eight-page submission to the MDBA slamming its use, presentation and interpretation of data in seven different areas including inflows, interceptions and climate change in the MDBA's guide to its proposed plan.

"There are a number of areas where ... the guide does not represent best-available science, or does not represent appropriate application of best-available science," the letter said.

"There are also areas where the explanations in the guide are either misleading or do not fully articulate key assumptions made by the authority."

The letter dismissed the MDBA's use of "interceptions" - water intercepted by farm dams and timber plantations before it gets to a river - in calculating new sustainable diversion limits as "logically inconsistent".

"The reporting of surface water balances in the guide is misleading," the letter said.

MDBA had overestimated the water which needed to be returned to the environment in some catchments, CSIRO said.

CSIRO said the guide failed to provide "convincing evidence" that the MDBA had the modelling tools to provide "optimisation of social, environmental and economic outcomes".

"Such capability could be quickly built from existing tools," its letter said.

It said the MDBA had failed to take into account the positive economic outcomes from the plan and could "lessen economic impacts" if "technical methods used to develop the plan are improved".

"The net cost of the plan should be compared to the net cost of not having a plan."

Victorian Farmers Federation president Andrew Broad said farmers with local knowledge had "been vindicated".

National Farmers' Federation natural resources manager Deb Kerr said the mistakes were "fundamental errors".

Australian Conservation Foundation healthy rivers campaigner Dr Arlene Buchan said the roll-out of the guide had been "a disaster" but was a "rough cut".

MDBA chief executive Rob Freeman said the MDBA had "worked closely with CSIRO" and that CSIRO's feedback was currently being considered.