Thousands more fish have died in a key river system in drought-hit eastern Australia just weeks after up to a million were killed, authorities and locals said Monday, sparking fears an ecological disaster is unfolding.

Fisheries officials said they were on their way to Menindee, a small outback town in far-west New South Wales state, after the third mass fish kill in the area in less than two months.

The town is near the Darling River, part of the Murray-Darling River system that stretches thousands of kilometres across several states and supplies the country's food bowl.

"There's lot of small (dead) fish... a lot of the larger fish have already perished in the last two kills," Menindee tourism operator Rob Gregory told AFP, adding that he counted 380 dead fish in just a six-metre (20-foot) stretch of river.

Gregory said Menindee was renowned as having one of the best fisheries in the far-west region.

"This is a true environmental disaster that is equivalent to a lot of other things that are occurring like the bleaching of the coral in the Great Barrier Reef," he added.

While the federal government blames the deaths on a severe drought, experts and locals say they stem from the systemic depletion and pollution of the river.

The NSW Department of Primary Industries said the latest kills were likely linked to rains and a sharp drop in temperature after an extended period of hot weather that contributed to plummeting oxygen levels in the water.

The state government has installed aerators in some waterways to keep the levels of oxygen up for fish, but Regional Water Minister Niall Blair said it was fresh water that was ultimately needed for them to survive.

"No scientists, no locals, no-one has been able to point to anything else that could prevent something like this other than fresh water coming into the system," Blair told reporters in Sydney Monday.

Opposition leader Bill Shorten called on the government to act, saying Monday the Murray-Darling was "facing the makings of an ecological disaster".

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