The cotton industry says it is not to blame for the mass deaths of hundreds of thousands of fish in the Darling River and is tired of being a “whipping boy” for problems associated with the drought.

Communities in the Menindee Lakes region, where two fish kills have occurred since December, have said over-extraction by irrigators helped cause the catastrophe that has put a spotlight on the environmental management of Australia’s largest river system.

On Thursday, New South Wales Labor called for a special commission of inquiry into the environmental disaster as the cotton industry sought to defend itself against criticism it was behind the depletion of river flows.

Cotton Australia said drought was affecting the river system and that the industry was also suffering, forecasting its crop this season would be half of the previous year’s.

“On the Barwon-Darling, the impact on cotton production is even more devastating with zero hectares of cotton being grown in Bourke this season, down from 4,000 hectares the year before,” the general manager of Cotton Australia, Michael Murray, said.

“Cotton Australia is very proud of our industry that produces a quality fibre that is in demand both here at home and around the world. But, as an industry, we are growing very tired of being ‘the whipping boy’ for all the problems that are being brought on by this crippling drought.

“The recent fish deaths in the Barwon-Darling river system at Menindee was a devastating sight. However, it is wrong to blame cotton growers for this incident.”

The immediate cause of the mass fish kill is believed to be a sudden drop in temperature that killed algal blooms in the water, depleting it of oxygen and causing fish to die.

But Richard Kingsford, the director of the Centre for Ecosystem Science at the University of NSW, said it was a disaster that had been many years in the making because too much water had been diverted from the system for agriculture.

“Droughts would have contributed to the blue green algae outbreak,” he said. “But the river droughts are happening more often and they’re more intense as a result of the irrigation industry in the Darling diverting water from the river over the last 10 to 20 years.”

He said the problem could be traced back to management of water by state and federal levels of government and both of the major parties.

The NSW Labor leader, Michael Daley, called on Thursday for the Berejiklian government to establish a special commission of inquiry into the state’s water management.

“The scale of this disaster is extraordinary and unprecedented,” the opposition leader said in a statement. “The people of NSW have watched for 18 months as water theft scandals, water mismanagement and now ecological disasters have rocked far west rivers.”

The NSW premier, Gladys Berejiklian, sought to assure residents of the state’s far west the government was working to find a solution.

Her comments come a day after the minister for primary industries and water, Niall Blair, was criticised for bypassing a large gathering of people waiting to ask him questions on a visit to Menindee.

“We’re working through it as fast as we can to see what solutions we can contribute towards and I commend him [Blair] for being on the ground,” she said.

Blair said this week he had met with residents in Menindee but bypassed the gathering on the town’s main boat ramp on security advice.