Fish will be cleared from "high density areas", but it will not be possible to remove all the carcasses, police say.

Police reassured local residents that the water supply remained "high quality". The deaths are thought to have been caused by low oxygen levels in the river after a recent heatwave.

An emergency hub has been set up in the town of Menindee in western NSW to co-ordinate the response and monitor water quality.

Describing the operation as "very challenging and significant", NSW Police Commander Brett Greentree said the event was "unprecedented in terms of the millions of fish which have died."

"Our purpose is making sure Menindee has clean water supply. I'm comfortable we're in a good spot regards to water quality at the moment," he told reporters.

Commander Greentree said contractors with specialised skills would use "a netting procedure" to remove the fish.

"But I need to be very upfront with the community and say 'will every fish be removed?' I don't think so, from the information I've had," he added. Posting a Facebook video showing rotting fish lining the riverbank, local resident Graeme Crabb wrote "the worst is still coming".