Peter Harris charged with two counts of extracting water when his metering equipment was not working

The New South Wales regulator has laid more charges against one of the state’s biggest cotton growers, Peter Harris, alleging that in August 2015 he extracted water from the Barwon river when the meters on his pumps weren’t working.

The documents filed in the land and environment court charge Harris with two counts of taking water when the metering equipment was not working, in contravention of the Water Management Act. The breach is alleged to have occurred between 6 and 8 August 2015 at a property called Mercadool near Walgett, and involves two separate pumps on the property.

Two types meters – one measuring the engine running time and the other measuring flow – were alleged to have been not working properly on both pumps.

This is the second round of charges brought against Harris since Four Corners first aired allegations that large irrigators were taking water illegally from the Barwon-Darling and the NSW government had turned a blind eye. An independent inquiry by Ken Matthews was scathing of the NSW government and recommended immediate changes to the enforcement function, which has now been taken over by the Natural Resources Access regulator.

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Harris and his wife, Jane, are also awaiting a verdict on charges that they pumped water illegally in 2016 at another property on the Barwon, Beemery Farm, when the river was low.

The water licence they held entitled them to pump water from the Barwon using up to four pumps but only when the flows in the Barwon-Darling system, as measured at the Bourke weir, exceeded 4,894 megalitres a day. If the river flow fell below that flow rate they were to cease pumping.

Each offence comes with a $247,500 maximum penalty. Harris did not return the Guardian’s calls.

Another irrigator, Anthony Barlow, pleaded guilty to pumping during an embargo designed to protect low flows, but claimed he had been told by the then water minister Kevin Humphreys that pumping was permitted. He was fined $190,000 for taking water in breach of the rules.

Meanwhile Harris and his wife Jane have brought action against the water minister, Melinda Pavey, over a refusal by the minister to authorise changes to the configuration of pumps at a third cotton property near Moree.

The Harrises had asked the department, which has the delegated authority of the minister, to authorise changes to their water access licence at a property, Kindamindi at Moree. It is understood the Harrises wanted to alter three pumps to improve their access to water. WaterNSW refused on behalf of the minister, saying that it would be a breach of the Barwon-Darling water sharing plan.

The Harrises have appealed the decision.

The new cases come as the newly elected Coalition government and basin states grapple with a worsening drought and deep concerns among the farming community about whether the Murray-Darling basin plan is delivering on its objectives.

The Murray-Darling Basin Authority (MDBA) has been under pressure whether it is taking a large enough role in enforcing the plan and ensuring states deliver on their commitments to provide detailed water sharing plans by mid-2019. NSW is running behind schedule on its 27 plans, and is unlikely to make the deadline.

There have also been ongoing questions during the election about the large water buybacks undertaken by the department in 2017 without tender.

The $80m buyback from Eastern Australia Agriculture, which operated two properties in Queensland, has been a particular focus because the company was founded by Angus Taylor, the energy minister in the last government, though Taylor had no role in or connection with the company after he entered parliament in October 2013. He also said he did not receive any benefit from the sale.The questions are ongoing and the transaction has been referred to the auditor general.

Following a five-year review of the plan by the Productivity Commission, the water minister, David Littleproud, said during the campaign that he was open to working with the basin states to discuss breaking up the MDBA to create a water management agency and a separate regulator, as NSW has done.

The PC’s five-year review into the management of the Murray-Darling basin said the dual roles of the MDBA were often in conflict.

“Those conflicts would only worsen in the next five years,” the PC report said. “The MDBA should be split into two separate institutions – the Murray-Darling basin agency and the basin plan regulator.”

Littleproud said he didn’t “necessarily” agree that there was a conflict of interest in the basin authority but, if he had evidence put in front of him, he was prepared to look at it.

“We will sit down with the states and work through that, I’m agnostic,” he said. “If we think we can get better outcomes, then we will. We have taken steps in terms of compliance.”

It is not yet clear whether he will retain the agriculture and water portfolio in the newly elected government.

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The Centre Alliance, which has two of the six crossbench senators, has signalled that it will make reform of the Murray-Darling one of the major issues in this term of parliament.

Senator Rex Patrick said he would continue to push for a royal commission into the Murray-Darling basin plan.

He is also going to begin discussions on a constitutional amendment to make the Murray-Darling a national responsibility.

“We need consistency of approach and we need a national perspective on management of the river system,” he said.