LEIGH SALES, PRESENTER: Australia will soon have the world's largest marine reserve but it could come at a cost.

The nation's commercial fishing industry says the Federal Government has gone too far in its effort to protect vast swathes of ocean. From next year, millions of square kilometres will be protected, forcing some fishermen to move or close down.

Here's Hayden Cooper.

DR SYLVIA EARLE, OCEANOGRAPHER: There's another whole Australia that most people don't fully appreciate. It's blue. And it is filled with life. There are fish there - nowhere else on Earth. Crabs there - nowhere else on Earth. Systems there - nowhere else on Earth. Just here.

We can't just continue to go round hacking away at the big blue engine that keeps us alive and still get away with it.

HAYDEN COOPER, REPORTER: It's been called the blue halo that surrounds the Australian continent. A spectrum of life that demands protection. But how much of the nation's waters should be quarantined?

BRIAN JEFFRIES, COMMONWEALTH FISHERIES ASSOCIATION: The Government proposals in this case are just extremism. This is the most radical proposals that we have ever seen.

SYLVIA EARLE: You have to keep thinking about Earth as this little blue speck in the universe. It's all there is. It's our only home.

BOB LAMASON, COMMERCIAL FISHERMAN: It doesn't make you feel very good and it doesn't make my staff feel very good.

HAYDEN COOPER: At the Cairns wharf fishing boats are returning. It's the end of another season. Time to take stock, carry out repairs and look ahead.

But the year 2012 will bring a moment of truth for the industry. A moment that long-time fishermen like Bob Lamason dread.

BOB LAMASON: We will be totally closed and we also run like the retail shop, we have a fish factory. We also supply wholesale into the town. But all that is generated from the fish that we catch. So without that we haven't got anything.

HAYDEN COOPER: The sentiment isn't confined to the far north. Australia's network of marine reserves is slowly taking shape and it stretches around the entire coastline.

The south-east was the first to be declared in 2006. Next comes the south-west. Half a million square kilometres of ocean will soon be protected. More reserves will be set aside in the north-west, across the top of the continent, and on the east coast.

But the Coral Sea reserve is the biggest of all. It will be the largest marine protection zone in the world. A million square kilometres will be locked away next year.

TONY BURKE, ENVIRONMENT MINISTER: We're not going to wait for everything to be endangered. Here's an area that is still relatively pristine. It's part of a great part in terms of environmental protection and biodiversity. Also part of our military history. And it's significant in its own right to not wait for things to be endangered but to actually protect it now.

BRIAN JEFFRIES: We never expected anything like this. I mean, what you're really looking at here is the Government's proposals would make Australia 45 per cent of the world's marine parks. And kick out an industry, basically fishing, which has the lowest carbon footprint of all protein sources. When you think about that, this is just contradictory and almost bizarre.

HAYDEN COOPER: Into this murky deep sea debate enters the interested American observer.

Dr Sylvia Earle is a renowned oceanographer and former chief scientist at the US Oceanic and Atmospheric Administration. She's in the country to lobby the Australian Government to stay the course.

SYLVIA EARLE: A plan is being put forward. Some will say, "Oh, that's too much." Others will say, "Oh, can't we do more than that?"

If the fish could vote, ha ha, if those in the future could vote, they'd be on the side of let's really do as much as we can to secure the special areas in the ocean.

HAYDEN COOPER: Dr Earle has been brought to Australia by the Pew Environment Group, an American think-tank that campaigns worldwide for marine protection.

The local fishing industry resents their involvement and their access to Australia's decision makers.

BRIAN JEFFRIES: Sylvia is a well-known radical proponent of marine parks. If you can't have them elsewhere, then grab Australia. Why do you think Pew are doing this? Why do you think Dr Earle is doing this? Simply because Australia is a soft touch.

SYLVIA EARLE: I used to give the fishermen kind of a hard time because I said, "You only value fish when they're dead. When they're swimming around in the ocean they have a zero accounting base but when you kill them, you take them to market, that's when they have a value."

There has to be a value for live fish not just dead fish.

HAYDEN COOPER: In the Coral Sea zone fishermen are now very much concerned with value. Like how much compensation can they count on from Canberra?

Some areas for fishing will remain. But they won't suit everyone.

BOB LAMASON: The nearest part of the Coral Sea that I can fish this is about 350, 400 miles from here and that doesn't mean to say that the fish are going to be there so you can steam for 400 miles at a hell of a cost and still find no fish.

SYLVIA EARLE: Of course I sympathise with those whose livelihoods depend on extracting ocean wildlife as a means of making a living. I'm really sympathetic mostly with those who are feeding their families, their communities. I'm less sympathetic with those who fish on an industrial scale. It's just big business.

HAYDEN COOPER: Big and small businesses are resigned to their fate. The Minister's determination to make it happen is crystal clear.

TONY BURKE: We will end up with the largest area in the world having a significant level of protection.

BOB LAMASON: If this is the process and this is what they want to do just get on with it and put us out of our misery.

SYLVIA EARLE: This is the time. We have maybe the next 10 years, the most important in the next 10,000 years, to shape a future that will work. Not just for the people of Australia who live here now, but for those who far into the future will look back on this time and say "Thank you."

LEIGH SALES: Hayden Cooper with that report.