Agriculture Minister David Littleproud is warning of more fish deaths in the Murray-Darling Basin this week and has called an emergency meeting of water managers to advise on how to avert mass killings.

Labor has branded the death of up to one million fish an "ecological disaster" and called on Prime Minister Scott Morrison to gather an independent team of scientists to urgently investigate the mass fatalities.

Meanwhile, a confidential document has revealed the NSW government was warned by its own experts in 2012 that water management rules under its proposed 10-year plan for the Darling River would put threatened species of fish, including the Murray cod, at risk.

Thousands of rotting fish carcasses have been found along a 40-kilometre stretch of the Darling River at Menindee, near Broken Hill in far-west NSW.

It has been described as one of the largest fish deaths ever recorded.