Rail operator Aurizon and the Queensland Competition Authority are at loggerheads over a draft ruling from the QCA in December that would allow Aurizon to recoup only $3.89 billion from its network business from July 2017 to June 2021. That figure was $999 million less than Aurizon wanted.

In response Aurizon, which has a monopoly on the state's coal rail network, has now said it would have to change its maintenance practices, leading to a reduction of up to 20 million tonnes in Queensland coal exports a year - or about 10 per cent of total exports.

It was expected the fight could cut about $500 million in Queensland government royalties each year, harming the budget bottom line.

The development came as another coal royalties drama was resolved this week, with BHP and the government reaching a confidential settlement on a $329 million dispute over a royalties reassessment.

Ms Palaszczuk on Tuesday urged the independent regulator and Aurizon to resolve the issue.

"I think it's very important that I reassure the Japanese government that their coal exports are secure," she said.

"I think it is very important that Aurizon and the QCA sit down and try to resolve this issue as a matter of urgency."

Ms Palaszczuk has asked her chief of staff to speak to representatives at Aurizon, and she will meet with the Japanese Foreign Minister Taro Kono in Tokyo, with the pair to discuss the problem.

Queensland Resources Council chief executive Ian Macfarlane said Ms Palaszczuk's call for Aurizon and the QCA to resolve the issue was "absolutely correct".

"The QCA's regulatory process is still under way," he said.

"We only have a draft decision on the table, yet Aurizon has already decided to choke coal supply to Queensland's customers, like the very worried steel industry in Japan."

But an Aurizon spokesman said the QCA draft decision made no commercial sense.

"They have recommended we drive our operational practices to the lowest possible cost regardless of the impact on our customers," he said.

"They have also recommended one of the lowest rates of return on any regulated asset in Australia."

The Aurizon spokesman said the company had to take action now because of the retrospective nature of the decision, which would be backdated to July 2017.

"And the very real prospect that it could cost Aurizon jobs and hundreds of millions of dollars if we don't," he said.

"However, we are trying to work with our customers and the QCA on a resolution to this matter as quickly as possible.

"We would urge the Queensland Resources Council to stop playing politics, do their job and help work with industry on a solution."

LNP leader Deb Frecklington said the government needed to sort out the dispute.

"This means a couple of billions of dollars to our bottom line in Queensland," she said.

"They need to make sure that they get the parties into a room and sort this problem out."

Treasurer Jackie Trad said the QCA was the right organisation to resolve the issue.

"Aurizon is a private monopoly, we need an independent statutory authority to determine what are the right charges for all users of that monopolistic infrastructure," she said.

Ms Trad said the state government had no statutory basis to intervene.

Aurizon has also launched an application for a judicial review in the Supreme Court, seeking to scrap the draft QCA ruling.

On Tuesday afternoon, the QCA released a consultation paper, asking for comments on maintenance and operational matters, and said it was "favourably disposed" to accepting Aurizon's revised claim for direct maintenance costs.

In a statement, the QCA said stakeholders had argued that greater accountability should be applied to Aurizon, in relation to its maintenance and operational activities.

The QCA said stakeholders should collaborate and provide joint submissions, where possible.

"The QCA encourages Aurizon Network and its customers to engage with each other in order to reach a pragmatic consensus on these matters," it said.

"The draft decision sought submissions from all stakeholders and did not represent any final views... The QCA's assessment may change when it makes its final decision."

Meanwhile, South32 on Tuesday announced it had signed a conditional agreement to acquire a 50 per cent interest in the Eagle Downs metallurgical coal project in Queensland's Bowen Basin.

The Queensland coal sector generated $36.2 billion in export revenue in 2016-17 and delivered $3.4 billion in royalty payments to the Queensland government.

Last year, Queensland exported $7.397 billion worth of coal to Japan, $9.971 billion to China and $7.724 to India and $4.139 billion to South Korea.

CORRECTION: A previous version of this story incorrectly indicated Premier Annastacia Palaszczuk would be meeting with Foreign Affairs Minister Julie Bishop. However, she was referring to Japanese Foreign Affairs Minister Taro Kono.