The Queensland Government is trying to sneak through legislation to reward a multinational miner that broke the law, while punishing a state-based company, a mine owner says.

Natural Resources and Mines Minister Anthony Lynham introduced an amendment to the Mineral Resources Act on Wednesday to allow Glencore to continue mining activities in an area of the Bowen Basin, which it had allegedly been using for more than 10 years without the correct authorisation.

Queensland miner QCoal has a mining lease application over the area and referred senior staff of the Mines Department to the Crime and Corruption Commission (CCC) for not stopping Glencore's activities.

QCoal managing director Chris Wallin said the approval for Glencore would significantly affect his $1 billion Byerwen project, which was shovel-ready.

"On the line here are 500 jobs for regional Queensland and $15 million a month in royalties for the state's economy," he said.

"It is gross public maladministration and outrageously unfair — this bill robs Queensland of hundreds of millions of tonnes of coal worth billions of dollars.

"The Mines Minister has not investigated these claims for well over a year and yet he's rushing through legislation — this is just unprecedented and shows a total disrespect for the law."

However, Dr Lynham told Parliament yesterday his amendments would resolve a longstanding commercial dispute between QCoal and Glencore by granting a transportation mining lease to Glencore to carry out their operations for a set period of time.

"These amendment also provide a framework for the QCoal project to go ahead in the manner and the timeframes that QCoal themselves have proposed as part of the application process," Dr Lynham said.

Opposition mines spokesman Andrew Cripps said the LNP had concerns about the amendment being introduced at the last minute, but would have to look more closely at the proposed changes.

"It always seems to me that when a government has to bring an amendment bill to the House that specifically names an individual resource tenure, that the House should be particularly cautious about the reasons why that has had to occur," he said.

Mr Wallin said it was "a warning to all companies wanting to do business in Queensland".

"This State Government makes the rules as it goes along and sovereign risk is now alive and well in Queensland," he said.