Federal and state ministers have rejected claims of mismanagement in the Murray-Darling Basin following the death of an estimated one million fish, described as one of the largest fish kills ever recorded.

Federal Agriculture and Water Resources Minister David Littleproud and his NSW counterpart Niall Blair said the drought was to blame for the disaster, which has centred on the outback town of Menindee on the banks of the Darling River.

Mr Blair was in Menindee on Wednesday and pledged his department would investigate the carnage, which was triggered by a cold snap that killed blue-green algae, reducing oxygen below critical levels.

But farmers, residents and some experts have blamed mismanagement by government and the Murray-Darling Basin Authority for repeated draining of the Menindee Lakes, leaving fish more vulnerable.