LEIGH SALES, PRESENTER: Australia's most loved environmental asset, the Great Barrier Reef, has faced many threats over the years. Everything from marine pollution to predatory starfish have endangered the world heritage listed site. Now massive port development s and dredging are fuelling concerns and UNESCO is considering listing the reef as in danger.

Against this backdrop 7:30 has learned of disturbing accusations about the body charged with protecting the reef, the Barrier Reef Marine Park Authority. Our investigation has revealed two of the Authority's board members have links to mining and resources companies that could benefit from port developments. They also have links to the family of infamous NSW politician Eddie Obeid who is currently facing another corruption inquiry.

At the same time, the authority board is accused of watering down its policy on protecting the reef against such developments. Conor Duffy has this exclusive report.

CONOR DUFFY, REPORTER: Clear waters, diving and famed white sands make the Whitsunday Islands a paradise for visitors from all around the world.

Dive master Tony Fontes was one of them. He came for a two week holiday, 30 years ago.

TONY FONTES, DIVE MASTER: I discovered the Great Barrier Reef. It was really quite simple. I left California in 1978, I had plans to travel the world as a backpacking dive instructor. Once I hit Australia that was the end of my plans and I've been here since.

CONOR DUFFY: Today he's heading to Manta Ray Bay for a dive spot that's one of the best in the Whitsundays.

TONY FONTES: Well, my favourite of the corals but your favourite is going to be the fish and you're going to meet a fish which is just about as big as you are but very friendly. Very friendly.

CONOR DUFFY: In this underwater world the fish wait to catch the eye and the feeds. There's coral as big as a house, the colours are rich and varied and with so many fish to go with the coral Manta Ray Bay is one of the best dives in one of the wonders of the world. But Tony Fontes fears this is at risk from developments up and down the Queensland coast.

TONY FONTES: We've got Abbot Point to the north which is quite small at the moment, but if it goes ahead as planned lit be the largest coal export port on the planet and if Mackay goes ahead it will be the second biggest port coal on the planet. And the Whitsundays lie in the middle.

CONOR DUFFY: Just 50 kilometres north of here at Abbot Point, plans are under way to build the world's biggest coal port with a final decision due in mid December. If the Federal Minister approves it, three million cubic metres of mud will be dredged up, and then dumped in the Great Barrier Reef world heritage area.

TONY FONTES: This is the spot along the reef that's closest to the port and of course I worry. I worry for the entire Great Barrier Reef but the Whitsundays is the jewel in the crown so with ports north and south we're kind of in the middle of a hard spot.

CONOR DUFFY: Charter boat operators are among a growing number of tourism businesses pushing back against the dredged dumping plans. There are fears the plumes from the dredging will travel here, muddying the famously clear waters, and even damaging reefs.

Charter boat veteran Tony Brown is organising a coalition of local businesses and is meeting with the Federal Environment Minister Greg Hunt tomorrow.

TONY BROWN, WHITSUNDAY CHARTER BOAT INDUSTRY ASSOC: Let's have a look at other options out there. Do we need to really dump the spoil in the Barrier Reef? Is it that necessary or is this just an economics that means it's a cheapest option and we can just go ahead and do this and forget about it?

CONOR DUFFY: The company building Abbot Point, North Queensland Bulk Ports, says a 2 year assessment shows the impact from the dredge will be limited. But another report commissioned by the Great Barrier Reef Marine Park, and disputed by the port, found the pollution can travel much further than previously thought.

TONY FONTES: Nobody knows the impact. They did some dredging in Gladstone, as many people are aware, based on science and the science was wrong. It has been a total disaster.

PROTESTER: Save our reef! Save our reef!

CONOR DUFFY: The debate is playing out up and down the cities hugging the Barrier Reef coast with dredging and massive port expansions planned in Gladstone, Mackay, Abbot Point, Townsville and Cairns. That will mean big dumps of contaminated mud throughout the world heritage area.

TONY BROWN: Looking at Townsville 5.6 million cubic metres, we're looking at Abbot Point of three million cubic meters, Gladstone 12 million cubic metres. Cairns is looking at five million cubic metres.

CONOR DUFFY: Last year dredging at Gladstone was blamed by local fishermen for a mass fish kill, though the port's operators dispute that.

TONY BROWN: When you look at Gladstone what happened down there, no one really knows what's created their problems. But we sure as hell don't want to have that issue happening again. And that would be just devastating.

CONOR DUFFY: The body that has the job of protecting the reef is the Federal Government's Great Barrier Reef Marine Park Authority. It's headed by a 5 person board but environmentalists are now accusing two of those board members of having a conflict of interest. The first is Queensland's top public servant Jon Grayson who represents the State Government on the board. He owns a one sixth share of a company called Gasfields Water and Waste Services founded in June this year.

LOUISE MATHIESON, GREENPEACE: This particular company stands to profit from the growth of the gas industry and the gas industry in order to expand wants to have massive new developments, particularly in Gladstone. So we think that there are questions about whether Mr Grayson would benefit from the expansion of gas ports in Gladstone.

CONOR DUFFY: Until two months ago one of the five other shares in Gasfield Water was owned by Eddie Obeid Jr, the son of notorious former NSW minister Eddie Obeid who was found to have acted corruptly in other mining deals.

Eddie Obeid Jr sold his stake in August. The other Marine Park Authority board member in the sights of environmentalists is former Labor candidate Tony Mooney who unsuccessfully ran for Federal Parliament in 2010. He was also Labor mayor of Townsville for 19 years and was appointed to the marine park Board by the Gillard Government in 2011.

TONY MOONEY, FORMER LABOR CANDIDATE: And I've got the experience to deliver.

CONOR DUFFY: Queensland electoral records show he received a $5,000 donation for his 2010 campaign from the Obeid Corporation. Mr Mooney's day job is here at Guildford Cole where he's a mining executive paid $250,000 as manager of stakeholder relations. The company plans to run six coal mines in Queensland.

Guildford Coal helped fund a feasibility study into the Townsville port expansion signing a memorandum of understanding with the port.

LOUISE MATHIESON: Tony Mooney gets paid up to $250,000 a year to manage stakeholders for a coal company. I'm sure it's a lot easier to manage a stakeholder like the Marine Park Authority if you sit directly on the board.

CONOR DUFFY: Tony Mooney denies there's a conflict of interest but told us he declared his employment with Guildford. The company's website still trumpets the port memorandum and also has this quote from Mr Mooney from a mining industry publication.

TONY MOONEY (VOICEOVER): "We think there is a niche opportunity for the export of some coal through the Port of Townsville, and we're obliged to look at that opportunity and to weigh that up exporting through the soon to be upgraded Abbot Point facility."

CONOR DUFFY: In March last year the Great Barrier Reef board held a critical meeting in Gladstone. Tony Mooney was one of five people present. Their job was to formulate the marine park's position statement on port development. It was to be a crucial document.

Before the board was a recommendation from authority scientists that took a tough line. The draft statement prepared by its experts read:

(Voiceover) "The authority will not support port activities or developments in locations that have the potential to degrade inshore biodiversity."

CONOR DUFFY: At the next board meeting, this time in Townsville on September 5, 2012, minutes record the board requested the position statement be changed.

Both Tony Mooney and Jon Grayson took part. The new watered down version dropped the reference to not supporting port expansions and instead said this:

(Voiceover) "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."

CONOR DUFFY: Environmentalists believe that change by the board is crucial and could decide whether a port development is approved or knocked back.

LOUISE MATHIESON: The port's position statement will guide the authority in how it applies the rules relating to port development along the coast. So it could make the difference between whether the authority supports a development or opposes it.

CONOR DUFFY: There is no indication of the position individual members took but Greenpeace campaigner Louise Mathieson says a number of clauses were weakened and believes both men should resign from the board.

LOUISE MATHIESON: I think it would greatly increase the confidence that the Australian public and the international community could have in the management of the reef if these two men stepped aside from the board. The new Environment Minister, Greg Hunt, was not responsible for appointing them, we'd urge him to take a close look at their interests and revisit the decision to have them on the board.

CONOR DUFFY: After the changes the position statement was approved and sent out for consultation with a request from the board for more extensive consultation with the mining industry. It still hasn't been publicly released.

In a statement the Marine Park Authority says board members with different qualifications lead to more robust debates and the changes to the position statement were appropriate.

(Voiceover) "The board asked for the change to the initial words as a matter of clarification, because if taken literally, they would mean opposition to any activity whatsoever, no matter how insignificant the impact might be."

CONOR DUFFY: John Grayson also declined an on camera interview but a spokeswoman for the Premier issued this statement to 7:30.

Queensland Premier's Department: (Voiceover) "The Queensland Government rejects any suggestion Mr Grayson has a conflict of interest. Following his appointment, and with accordance with the Queensland Integrity Commissioner's advice, Mr Grayson ceased to have any managment involvement in active companies.

"His retention of passive interests is in accordance with the Commissioner's advice and poses no real or potential conflict of interest."

CONOR DUFFY: Former Marine Park Authority board member Daniel Gschwind is worried by the weaker position on ports.

The is that something that would concern you?

DANIEL GSCHWIND, TOURISM QUEENSLAND: Absolutely, port development is one of those things we can influence. We know from the science which has been very strong over the last few years, over the last couple of decades, very much more supportive of the kind of debates that we're having. We know from that science that one of the great man made threats to the reef is sedimentation, is water quality.

TONY FONTES: I can remember coming here near 30 years ago and it used to be a really nice dive site.

CONOR DUFFY: Back in the Whitsundays, Tony Fontes is showing his son Taylor a reef that locals believe has been damaged by dredging on a much smaller scale than Abbot Point. They capture footage showing murky water quality and a much diminished dive.

TONY FONTES: Although the dredge spoils were tipped onto land, not into the sea, the disturbance of the seabed loosened up the soil and now, and this was about two point five, three years ago, any time you get, not even a big weather event, just a strong wind you will see the sediment rise up and move off shore and some of the nearby islands the visibility has been compromised for the last three years from a very small dredging.

CONOR DUFFY: With major decisions on ports looming up and down the coast, many on both sides are gearing up for a fight that could get dirty.

LEIGH SALES: Conor Duffy reporting. Late today a spokesman for the Environment Minister Greg Hunt told 7.30 he has ordered an immediate probity inquiry into Labor's appointment of Tony Mooney to the Marine Park Authority board. Mr Mooney and Jon Grayson declined to be interviewed, as did the Marine Park Authority and the ports operators.

Read the written statements provided to 7.30 from the Great Barrier Reef Marine Park Authority, the North Queensland Bulk Ports Corporation, and the Port of Townsville Limited.

Editor's note (Friday 16 May, 2014): read the report by Mr Robert Cornall AO into Jon Grayson and Tony Mooney.