Miners have been paying a larger proportion of tax in Queensland for coal sold for more than $175 per tonne since the start of July.
The state government says the regime is fair after a 10-year freeze but miners and Japan's Ambassador to Australia Yamagami Shingo have criticised the change.
Mr Shingo says the unexpected hike could impact Japanese firms' investment plans in Australia.
He warns that this includes hydrogen production and shipping joint ventures such as the $500 million Hydrogen Energy Supply Chain in Victoria's La Trobe Valley.
"I stand by my comments that the royalty hike has affected the trust Australia has built up with Japanese investors," Mr Shingo said in a speech at the Minerals Week 2022 conference in Canberra on Tuesday.
"It could have implications beyond Queensland or the coal industry, affecting Japanese investment in joint ventures.
"Indeed, the Queensland government's announcement sent shock waves through Tokyo, causing a drop in the stock price of one of the major Japanese trading companies."
Kawasaki Heavy Industries and Queensland's state-owned Stanwell Corporation are also conducting a $10.4 million feasibility study on producing and shipping hydrogen.
The Japanese firm has also signed a memorandum of understanding for a hydrogen export project at the Port of Townsville.
The Queensland government has said the hydrogen joint ventures are a key part of its plans to meet net zero emissions targets by 2030.
Mr Shingo said last month he met with Premier Annastacia Palaszczuk to ask her to consult more with Japanese companies operating in Queensland.
"And not long after, state Treasurer Cameron Dick conducted a face-to-face meeting with Japanese businesses," he said.
"While this is a step in the right direction, a lot remains to be done.
"Japan will continue to follow this issue closely."
The Queensland Resources Council, the state's mining lobby, said the government's lack of consultation on the coal tax hike had spooked Japanese investors.
QRC chief executive Ian Macfarelane said the state needed foreign investors to develop industries like hydrogen and rare earth minerals needed for renewable energy generators.
"But the Ambassador made it clear Japan is rethinking its investment plans for Queensland, firstly based on the way they've been treated and secondly because the government has changed the goalposts on them without any consultation, which has affected their return on investment," he told AAP in an emailed statement.
"You just can't do that if you want companies to invest in Queensland in the long term."
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