A leading former scientist with the Department of Natural Resources and Water has lashed out at "flawed" mining application processes in Central Queensland, which he says are putting the Fitzroy Basin's waterways and flood plains at major risk of contamination.

Bob Noble, who has just retired from his position as principal scientist in the central west with DNRW after 40 years in State Government departments, has spoken out about what he believes is major hypocrisy in the Government's treatment of the mining sector as opposed to agriculture.

For the past 20 years, Mr Noble has had responsibilities in the Fitzroy Basin and Mackay Whitsunday regions to help monitor and minimise the human impact on water quality, river health and the Great Barrier Reef.

He said agencies including the DNRW and the Environmental Protection Agency (EPA) were failing to recognise the importance of the area's major stream network, riparian zones and flood plains when considering mining development applications, and not enforcing substantial setback areas for mines.

"I've worked with the agricultural sectors for many years on these issues and believe that much progress has been made through environmental audits and best management practices," Mr Noble said.

"I've also argued within DNRW that there seems to be two sets of rules for development applications in the region that may impact on streams, riparian zones and flood plains.

"There's one set of rules for the agricultural sector and others who may propose activities adjacent to major streams, and a second set of rules for mining.

"It gives me no satisfaction to see the current impact of coal pit water from Ensham Mine (at Emerald) on water quality of hundreds of kilometres of streams in the Fitzroy system – the Mackenzie and lower Fitzroy, from Ensham to the Barrage at Rocky – and the implications for irrigation, the aquatic environment and drinking water supplies for rural towns.

"I'm apolitical, but the reality is someone has to question the environmental credentials of the current State Government.

"I really think its Third World country stuff that’s going on."

* Extract from a special report in Queensland Country Life, October 2 edition.