The environment minister, Greg Hunt, has ordered a probity inquiry into allegations from environmental groups concerning potential conflicts of interest of board members of the Great Barrier Reef Marine Park Authority.

In a report which aired on the ABC’s 7.30 on Tuesday, Greenpeace raised concerns about two Great Barrier Reef Marine Authority board members – Tony Mooney, a former mayor of Townsville and unsuccessful federal Labor candidate for the seat of Herbert, and Queensland public servant Jon Grayson, the Queensland government representative on the board.

Mooney is an executive for Guildford Coal and Grayson, according to the ABC, owns a share of a company called Gasfields Water and Waste Services. Greenpeace alleges the two men have links to resources companies that would potentially benefit from contentious port expansions currently being proposed in north Queensland, and that raises the potential for conflict of interest.

The environmental group is pointing to a March 2012 meeting of the authority board to formulate a “position statement” on future port development. The ABC reported that marine authority scientists proposed tough wording at the March meeting. “The authority will not support port activities or developments in locations that have the potential to degrade inshore biodiversity.”

Then at a meeting in September 2012, the port development position statement was watered down. The ABC said the amended statement dropped the explicit reference to not supporting port expansions after a request from the board. “The board requested that the position statement be changed, to in making decisions regarding port development, the potential impact on inshore biodiversity should be a key consideration.”

Mooney has denied any conflict of interest, and said his employment in the coal industry had been declared. The Queensland government has backed its representative, saying Grayson has no conflict of interest, and is not involved in any active company management.

Greenpeace’s Louise Mathieson has called for the men to stand aside from the board, and that call was echoed on Wednesday by the Greens leader, Christine Milne, who called for a halt to development. “We shouldn’t be proceeding with the Abbot Point expansion,” she said.

The Abbot Point coal development – if approved over the next few months – would be the largest coal port in the world. Given the fragile state of the reef and its economic value as a tourist destination, port expansions and dredging up the coast has pitted tourism operators against resources interests in Queensland.

The Australian Marine Conservation Society has called for an investigation to be conducted by the Crime and Misconduct Commission. Felicity Wishart, society’s Great Barrier Reef campaign director, said an investigation would provide confidence about the “separation between decision makers and mining interests”.

“Allegations raised on the 7.30 report are very serious and affect confidence in the entire industrialisation of the Great Barrier Reef’s coastline,” Wishart said. “There is now a shadow of corruption over the development agenda and all Queenslanders need to be assured that this is not the case.”

“Plans for mega-ports along the coast have been fast-tracked and given special treatment by government. We need to know exactly who is benefiting from this port development. The CMC should investigate the role individuals and government played in fast-tracking developments and approvals,” she said.

A spokesman for Hunt said: “All appointments to the board were made prior to this government, and the minister has ordered an immediate probity inquiry into all allegations made.”