There will be an independent investigation into allegations two Great Barrier Reef Marine Park Authority (GBRMPA) board members have a conflict of interest due to ties to mining companies.
Former Townsville mayor Tony Mooney and the director-general of Premier Campbell Newman's department Jon Grayson have both been linked to mining companies.
Documents obtained by the ABC show the GBRMPA has taken an increasingly weaker position on new port developments near the reef.
Federal Environment Minister Greg Hunt says, although the appointments were made prior to the current government taking office, it's his job to ensure there is an external independent inquiry.
"Both of the gentlemen in question have strong reputations and I don't want to draw any judgment in any direction," he said.
"My task, our duty, our responsibility is to have them investigated."
GBRMPA makes recommendations to the government on a number of large-scale port developments along the Queensland coastline.
The Greens have called for both men to stand down during the investigation to ensure the public has confidence in the management of the reef.
But federal MP Ewen Jones says Mr Mooney has every right to sit on the board, adding he wouldn't have been appointed because of his coal contacts.
"I think he was appointed to the board because of his long and fantastic commitment to north Queensland and I think any board must have a cross-section of views," he told ABC Radio on Wednesday.
Mr Mooney was the mayor of Townsville for 19 years and ran for federal Labor in 2010.
He's an executive for Guildford Coal and Mr Grayson is reported to own a share of a company called Gasfields Water and Waste Services.