Narration: On January 7, 2006, 4 people left the safety of their mothership to put themselves between a whale and death.

Shane Rattenbury: The first two shots completely missed the whale. The third shot then left a gaping wound. We could see the whale still desperately trying to escape.

It was 35 minutes between the first time it was struck by a harpoon and when it died.

It's a really gut wrenching moment and a terrible sense of failure when you realise that whale you've spent the last two hours trying to protect its come to an end.

Narration: This is the picture Greenpeace showed us of Japanese whale research.

Dr Jonica Newby, Reporter: It sure provokes emotion, but when it comes to science, shouldn't we look beyond sentiment? Aren't you curious what the Japanese research program is about - what they've discovered? Well we are. So we've gathered just about every paper they've ever produced. We're going through the lot as we investigate the science of scientific whaling.

Narration: We've come to the old whaling town of Hobart - taken a room - and assembled a panel of experts.

Dr Nick Gales, scientific committee member of the International Whaling Commission, and a reknowned scientific whaling critic

Professor Pat Quilty, former chief scientist of the Australian Antarctic program -

and UNSW Dean of science, Professor Mike Archer. He's had nothing to do with whales, and favours harvesting wildlife.

Dr Jonica Newby, Reporter: this is it guys, the judgement room.

They're not allowed to leave this room until they've delivered their verdict.

Prof Archer: It's quite a pile

Dr Gales: it's a big pile

Prof Archer:Well I think the first thing we've got to do is look through every one of those papers and decide which ones have been peer reviewed. Because if they haven't been peer reviewed they don't have credibility in the scientific community

Prof Archer: Unrefereed, unrefereed

Narration: So how did scientific whaling come about?

To manage the exploding whale industry, in the 1940's, the International Whaling Commission was established.

By 1970, it was clear it had failed spectacularly.

Nick Gales The populations were so decimated that species like the Antarctic Blue Whale - the greatest largest animal that ever lived - are still just one percent of what they were prior to whaling days. We very nearly wiped out many of the species.

Narration: In 1986, the IWC bit the bullet and banned all whaling worldwide with a small exception whaling under special permit for scientific purposes.

Nick Gales: The problem is that any country can issue itself whatever number it wishes of whatever species it wishes to take say it's for scientific purposes and it can then legally go about taking those whales.

Narration:The first Japanese research program known as JARPA lasted 18 years. It finished mid 2005. So what has it produced?

Nick Gales: I've finished mine guys.

Well we've divided them now into the unrefereed papers and the papers that have been through a peer review process. And there's 55 of those. We've been fairly generous. Where we're not sure we've given them peer review status

Dr Jonica Newby, reprter Well this project took 18 years and cost hundreds of millions of dollars, how does that publishing output rate?

Nick Gales: Well it's poor.

Narration: Then again - never mind the quantity what about the quality?

Dr Jonica Newby, Reporter: So now, we're going to separate out the really useful papers from the useless.

Mike Archer: Oh here's a ripper. Fertilisability of ovine, bovine, that's sheep cows and minke whales spermatazoa intracytoplasmically injected into bovine oocytes. This is taking whale genetic material, putting it into cows. Oh man

Nick Gales: Can you picture the offspring.

Narration:While they're doing that, we thought we'd cross to Tokyo and find out what the Japanese themselves think are their most important discoveries.

Mr Joji Morishita is spokesperson for Japan's whale research program.

Joji Morishita: JARPA 1 had several important discoveries. We found the population structure of minke whales in Antarctic is very healthy - a lot of young animals. This population will thrive in the future. And number two is we are detecting the change in the ecosystem of Antarctic Ocean. The minke has increased but now other larger whales have been increasing and only JARPA can detect those changes. And number three good news is very low level of contaminants in minke whales

Narration: The Japanese make no bones about it - their research is toward that longed for day when commercial whaling is resumed.

Joji Morishita: The whole aim of our research activities is to establish sustainable whaling in Antarctic Ocean

Narration: So our panel are judging these papers on their usefulness for managing commercial whaling.

Nick Gales: There you are, that's my pile.

M: OK and that's my pile.

Pat Quilty: And that's our pile.

Well of the original 55 we're down to 14 that could be relevant.

Narration: Finally, our panel will separate out the papers that could only be produced by lethal research.

Because let's face it - the real source of contention is how many whales were killed for this information

6,800.

Joji Morishita: We need this number of samples in order to get statistically significant data. There are many pieces of information that can only be obtained from lethal sampling.

Narration: Nick Gales has spent the last 5 years of his scientific career trying to prove that wrong.

Earlier, he took me to a site that a hundred years ago teemed with whales to demonstrate how.

Nick Gales: So this is the system we've developed to collect whale faeces.

Dr Jonica Newby: so that's actually whale poo there?

Nick Gales: this is blue whale poo and contained within that is the DNA of whatever they've been eating.

Dr Jonica Newby: It's a lot simpler than killing whales.

Nick Gales: Well it is.

Narration: While this method yields dietary information to get gender, reproductive status, and population profiles, they take biopsies.

The only information that can't currently be obtained without killing, is age.

Joji Morishita: The age determination is now only reliably done by looking at the ear plug in the head of the animal. And you know to take this out you have to sample the animals.

Nick Gales: But the important point is that within the IWC, you don't need that age data. To establish a catch limit for whaling you need information about population structure, abundance and prior whaling history. You don't need age data.

Narration: As the sun slips over the yardarm, our panel are nearly ready to deliver a verdict.

Group: OK what have we got. That's one another two papers there and number four

Prof Archer: Alright, that's it. And from that whole pile of papers we've got a total of one, two, three, four papers that can be said to be peer reviewed, that have some relevance to developing or managing a whaling industry and also would require lethal sampling of whales to get that information. Just four papers.

Nick Gales: So with the eighteen year program and sixty eight hundred whales divided by four papers - that means 1700 whales killed for each one of those four papers.

Mike Archer: Extremely depressing. Nick Gales: It wouldn't pass an ethics committee. Archer: No it would not.

Dr Jonica Newby: So - the verdict - science or smokescreen?

Mike: I have to say, having seen it all it's more like a smokescreen than science.

Narration: But are there mitigating circumstances?

Has Japan been forced to resort to a sham by unreasonable cultural opposition to commercial whaling?

Joji Morishita: In Australia many wildlife animals are used killed used like kangaroos in a sustainable manner. We have no problem and I think for those people who accept the kangaroo hunting should accept sustainable whaling.

Narration: It's a really good point. But no one would suggest kangaroos are endangered.

That argument was undermined last year, when Japan announced it's new research program JARPA 2.

It doubles the Minke catch, and for the first time, includes endangered Fin and threatened humpback whales.

Nick Gales: As soon as JARPA 2 has now included threatened and endangered species then there become serious conservation questions as well as the scientific criticism.

Narration: It's why Greenpeace made the snap decision to relaunch their anti-whaling campaign in Antarctica

It's also why this year's IWC meeting, which begins June 16, is expected to be even hotter than last year's fought with both science and passion between the nations that believe whales are a resource, and those that believe humans did a wrong to whales that must never be repeated.

Nick Gales: you know these species are animals that have been driven to very, very small numbers in the past to be starting to take them after only a couple of decades of protection is quite premature.

Joji Morishita: I'm very looking forward to see the IWC to be normalised so that IWC can manage whaling, can protect depleted species and can allow the sustainable whaling to come.