The Queensland Resources Council says mines in the central part of the state have been inundated with water from the heavy rains, causing a halt in coal production.
The council's chief executive, Michael Roche says the export of coal to countries in Asia and Europe is also being delayed due to damage caused to railways linking mines to the state's shipping ports.
Queensland's premier Anna Bligh says the floods will have a long term effect on the state's coal industry.
Australia is the world's largest coal exporter supplying the valuable commodity to more than 30 countries across the world, including Japan, South Korea, China, India and Europe.
The flooding crisis has resulted in a number Australian coal mining companies, including Rio Tinto, BHP Billiton, Anglo American and Xstrata, implementing force majeure clauses contained in their delivery contracts.
Global Commodities Specialist, Macquaire Commodities Research predicts the coal prices may increase from USD 246 a ton to USD 300 a ton. Besides, a limited availability of coal could also generate a steel shortage, and a strong increase in the price of steel.