The New South Wales government has given the green light to irrigation farmers in the north-west of the state to harvest the recent rainfall, pleasing some but causing anger in towns such as Menindee and Wilcannia and on the lower Darling where the river has not flowed for a year.

The lifting of the embargo for three days will be welcomed particularly by cotton farmers who have lobbied the NSW water minister, Melinda Pavey, warning that unless they are able to harvest the water their infrastructure will be damaged.

Floodplain harvesting, which is unlicensed in NSW, is done by using levees, channels, gates and pumps to direct water into large on-farm storages, which are used for irrigation.

But it means the water is unlikely to find its way into the Darling, especially the lower Darling, causing anger downstream.

“It’s more than anger, I am heartbroken,” said Graeme McCrabb, a local resident of Menindee who has led the charge on raising awareness of the mass fish kills that occurred last summer and have continued to occur this summer.

“You should see it: mussels dying on the side of the river, dead fish every day. Words just don’t describe how terrible it is here,” he said.

“We are putting all this effort into relocating fish to save them, but now there won’t be any flush of the river and the environmental disaster will keep unfolding.”

He said towns such as Menindee and Wilcannia felt abandoned.

The Barka elder Badger Bates, who grew up at Wilcannia, said the native titleholders were really upset.

“Now we have a chance of getting a bit of water into the Barka [the Darling] but we’re not going to get it,” he said.

He said governments had released environmental flows as “shut-up water” but the river, which is at the heart of the Barka people’s spiritual beliefs, required a proper flush all the way to the junction with the Murray to restore it.

The NSW Department of Planning Industry and Environment issued the notice on Tuesday saying that “over the last three days in excess of 250mm in some locations across the Namoi and Lower Gwydir had resulted in large volumes of overland flow on the flood plains as well as flash flooding”.

The exemption applies to irrigators in the Namoi floodplain, the Gwydir floodplain and parts of the Barwon floodplain to harvest overland flows on their properties.

The department said in the notice that flow targets had been met in the Namoi and “might be met at Wilcannia”.

But it said that “flow forecasting indicates flows will not be adequate enough to provide any flows into the lower Darling system”.

The Darling River in Louth, NSW. No flows have yet reached the town from the recent rains upstream. Photograph: Kathy Barnes

Stuart Le Lievre, the vice-president of the NSW Floodplain Association, which represents farmers other than irrigators, said it was “a dreadful decision” and possibly illegal because the water-sharing plans put water for towns and stock ahead of water for irrigation.

The government has kept water restrictions in place for the Sydney basin despite dam levels rising to 62% while it assesses the impact of the rain and likely forecast falls.

But it has allowed immediate harvesting in the north-west of the state, where the majority of cotton is grown.

Just six days ago Pavey criticised Queensland for allowing irrigation farmers to opportunistically pump water from its rivers, which are flowing for the first time in years. NSW said is was monitoring the activity via satellite surveillance.

Earlier this month, in anticipation of big rainfall, the NSW government imposed an embargo on irrigators taking water from rivers in the northern river valleys.

“We have embargoed farmers from pumping water in the northern basin to supply critical human needs, as well as providing replenishment flows for remnant pools in riverbeds,” Pavey said.

“I have made it clear that until the rivers have sufficient water to provide those downstream a drink, it would be inappropriate to start the pumps up and stop water flowing­ across the border.”

But allowing floodplain harvesting in NSW will have a similar effect. The practice, which is largely unregulated in NSW, is thought to result in less than 40% of rainfall reaching the rivers.

Pavey said the suspensions were only temporary and restrictions were expected to be put back in place by Friday.

She said the Natural Resources Access Regulator (NRAR) and the Flood Plain Harvesting team were surveying the region by air on Tuesday to investigate the extent of flooding and check the claims of infrastructure damage.

“It is a relief to see naturally occurring flows running all the way down the Barwon River from Mungindi to Walgett, likely to replenish town supply weirs at Brewarrina and Bourke and we’re hopeful even down to Menindee Lakes,” Pavey said.

However the Greens said it defied logic to start harvesting overland flows.

“When parts of the Darling are still dry, it defies logic that corporate upstream irrigators would be permitted to pump water and harvest floodplains, preventing precious flows from making it downstream,” the Greens water spokeswoman Sarah Hanson-Young said.