A Productivity Commission report found the GST deal struck in 2018 by the Morrison government was "perverse" and costing federal taxpayers more than $6 billion per year to fill up WA's coffers.
Following the report's release, WA Premier Roger Cook launched a scathing attack on the commission.
"On the Productivity Commission, you do not have a single representative from Western Australia, and it's clear from their report that they don't get Western Australia," he said at the time.
The report, he said, was the work of "east coast clowns".
Prime Minister Anthony Albanese has since promised to keep WA's GST deal intact.
"I think that Western Australia deserves its fair share," he said after a meeting of National Cabinet on Wednesday.Â
"People are aware of my position on that, but I support every state and territory."
Dr Chalmers said the prime minister had done no wrong in ruling out changes to the GST arrangements before the commission had released its final report.
But he said Mr Cook's comments were not appropriate.
"You can disagree with the conclusions of the Productivity Commission without denigrating them," Dr Chalmers told reporters in Logan.
"It's important that even when those conclusions are contested - as they often will be - we continue to respect the people of the Productivity Commission and the really important work that they do."
Dr Chalmers has a close relationship with commission chair Danielle Wood, who has been a key supporter of Labor's progressive economic agenda since he appointed her to the role in 2023.
Mr Albanese's description of the commission as "economic rationalist" was not a criticism, Dr Chalmers added.
"I don't consider what the prime minister said to be inappropriate, but I think some of the other commentary around it has been unfortunate," he said.
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.
"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."
Dr Jackson conveyed her concerns in a meeting with WA Treasurer Rita Saffioti in Melbourne.
The body will still take feedback on the GST proposal before it hands down its final report by the end of 2026.
