An unprecedented dispute has broken out between Water Minister Melinda Pavey and the state government's Natural Resources Commission, which has privately accused her of "shooting the messenger" after it warned of the dire state of the Barwon-Darling river system.

Natural Resources commissioner John Keniry on Monday wrote to Ms Pavey to complain about public concerns she raised about his agency's review of the Barwon-Darling water sharing plan, which had concluded changes made by the Coalition had put the river at serious risk.

"Never in my time as commissioner have I been publicly criticised by a Minister for the quality or process of our work," Dr Keniry wrote in the letter sent to Ms Pavey, Planning Minister Rob Stokes and Environment Minister Matt Kean and obtained by the Herald.

Water Minister Melinda Pavey is at odds with Natural Resources Commissioner John Keniry. Credit:Joel Carrett

"I fear you Minister are 'shooting the messenger' for the failures of the 2012 Water Sharing Plan."