Miners have been paying a higher proportion of tax for coal sold for more than $175 per tonne since the start of the new financial year.
In a speech at the University of Queensland on Wednesday, ambassador Shingo Yamagami said companies are now uncertain about investing in the state.
Resources Minister Scott Stewart has downplayed the diplomat's comments, saying increasing coal taxes is in the interests of Queenslanders.
"They're his comments, and he's obviously looking after the companies from Japan, and he's welcome to those comments," Mr Stewart told reporters on Thursday.
"But we need to make sure that we look at those multinational companies, looking at those super profits they're making, and some of that money that's owned by every single Queenslander - bringing that back to our communities to provide for our schools and our hospitals."
Ambassador Yamagami said some Japanese companies are questioning whether Queensland is still the safe and predictable place to invest it has been for decades.
He warned the coal tax hike could have widespread impacts beyond Japan's coal industry, in sectors such as hydrogen and infrastructure.
Queensland Opposition Leader David Crisafulli said he will meet with the ambassador on Friday to try to repair ties with Queensland's biggest trading partner.
Mr Crisafulli said Mr Yamagami's comments reflected how the state's global trading partners felt about the government's unpredictable policies.
"One of the foundations of our economy has been built on a lack of sovereign risk," he told reporters.
"These actions undo that, and whilst we can't change the betrayal, our partners feel we can prevent it from ever happening again in the future."
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