A Productivity Commission report found the "perverse" GST deal struck in 2018 by the Morrison government had cost federal taxpayers $23 billion in top-up payments to WA so far and said it needed to be scrapped.
Following the report's release, WA Premier Roger Cook described the commission as "east coast clowns" and said the recommendations were an attack on the state.
Prime Minister Anthony Albanese has since promised to keep WA's GST deal intact.
Productivity Commissioner Angela Jackson said Mr Cook's comments about the report went too far.
"Our view is that a line was crossed in terms of the nature of those comments from the Western Australian premier ... he also called the report deceitful," she told ABC Radio on Wednesday.
"To undermine and, I guess, attack our integrity ... is an additional bridge too far, and ... something more broadly we are seeing in public debate internationally.
"We want to call this out as being unacceptable."
Dr Jackson will meet with WA Treasurer Rita Saffioti in Melbourne on Wednesday, where concerns about Mr Cook's comments will be conveyed.
The commissioner said the prime minister's comments about keeping the GST deal for WA was disappointing but agreed the commission's staff were "economic rationalists", as described by Mr Albanese.
"It's important for us to indicate that that process will not be influenced by the prime minister's comments," Dr Jackson said.
"I would say that yes, we are economists. I hold a PhD in economics, as does my colleague Dr Alex Robson … so we are definitely economic rationalists."
The body will still take feedback on the GST proposal before it hands down its final report by the end of 2026.
Industry Minister Tim Ayres said while the comments from the WA premier towards the commission were colourful, different points of view should be welcomed.
"We're an Australian democracy. We should be we should be comfortable and confident about the way that we engage with each other," he told ABC Radio.
"The Productivity Commission's got important work to do, and the government will continue to respect the role of the Productivity Commission."
The issue of GST is likely to feature heavily at a meeting of state and territory leaders at national cabinet on Wednesday.
Other premiers and chief ministers have called for a more equitable GST deal.
Northern Territory chief minister Lia Finocchiaro said the territory needed its fair share of the tax.
"Ultimately, the territory actually has a different proposition it needs to put forward to the federal government above and beyond the GST contribution we currently get," she said.
"We rely very heavily on GST just to be able to keep the day-to-day operations moving."
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