The state government department told the company "several issues have not been adequately or fully addressed" in the Environmental Impact Statement for the project.

A Whitehaven spokesperson said it's a standard part of the EIS process for proponents to work with government to resolve technical questions.

Boggabri landholder Richard Avendano said the public submission didn't give local farmers much confidence in the company's protection of local water resources.

"How can you play with our most precious resource when it's guesswork?" he said.

"A letter like that raises enough doubt that this project isn't even ready to go to an EIS, or anything like that."

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He said water was the most precious resource for his farm, and he was concerned the new mine would threaten his access to groundwater, which was already stressed in the recent drought.

"There's huge pressure on our underground aquifers already," he said.

"We've got the cumulative effect of this proposal of the existing mine, this proposal and already Santos. The modelling is just so inaccurate."

Whitehaven had acknowledged that wells on his own property would be affected by the project, and he didn't have any confidence in its ability to "make good" the loss of water because he doesn't think the company will exist in a decade.

A Whitehaven spokesperson said the company had been consulting closely with DPIE-Water on its review of our modelling and are confident DPIE's feedback will be fully and adequately addressed in the company's response to submissions.

"The technical peer review process underpinning the assessments framework in NSW is why it is rightly regarded as one of the most stringent anywhere in the world," she said.

The company had "inadequate groundwater entitlements held", didn't explain subsidence impacts to watercourses or drawdown and water quality impacts of the project, according to the government submission.

"Comprehensive update of the water management plan required," the submission said.

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Whitehaven's assessment methodology for establishing a baseline for water-quality was "inadequately defined", it said.

And a number of other scientific monitoring processes are "not given in the EIS" or "not provided", the department said.

The extension project would expand the mine's longwall and extend the life of the mine to 2044.

The Narrabri mine, which opened in 2012, is currently due to wind up in 2031.

The DA and EIS for the mine extension received far more support than opposition through the public consultation stage of the development process.

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