A Queensland environmental organisation has launched a legal challenge against a major dredging project they say threatens the health of the Great Barrier Reef.

The Mackay Conservation Group filed a complaint against the dredging and dumping of three million cubic metres of spoil from the Port of Abbot Point at the Federal Court in Brisbane yesterday. 

Mackay Conservation Group coordinator Ellen Roberts said Federal Environment Minister Greg Hunt has a legal obligation to protect the Great Barrier Reef. 

"Australian environmental law says the minister has to protect World Heritage listed areas," Ms Roberts said. 

"The dredging and dumping of spoil, violates world heritage provisions.

"So if the case is successful it could have implications for other World Heritage areas across Australia."  

Ms Roberts said sediment from dredging will negatively impact the Great Barrier Reef. 

"We have concerns about what it means for local marine ecosystems," she said, "the decrease in water quality as a result of the dumping and the marine life that lives there."  

This is the second legal challenge mounted against dredging at Abbot Point, with the Queensland Conservation Group appealing the Great Barrier Reef Marine Park Authority's approval of the project. 

Ms Roberts said funds to make a legal challenge had been raised by individuals through advocacy group GetUp!. 

Around $150,000 has been raised by the group so far. 

"People are concerned about the scale of the increase in sediment is going to have," Mr Roberts said of the donors. 

But Queensland Resources Council's Chief Executive Michael Roche said the legal action has nothing to do with saving the Great Barrier Reef. 

"It is time to put an end to the charade that this activist campaign is about saving the Great Barrier Reef when it is really about shutting down Queensland’s coal and gas export industries," Mr Roche said in a statement.

Mr Roche said the parties named in the action are signatories to a strategy document released in 2012, titled 'Stopping the Australian Coal Export Boom'.

"Wildly exaggerated and scientifically unsupported claims over the impacts of port development and maintenance on the Great Barrier Reef are the means to an end – and that is the closing down of the Queensland coal and gas industries," Mr Roche said.