SARAH FERGUSON, PRESENTER: After a series of scandals, the live animal export trade is supposed to be enjoying a boost, with strong support from the new government and the recent reopening of key markets in the Middle East.

But now there are allegations that some rogue traders may be putting the whole industry at risk.

A 7.30 investigation has discovered a trail of paperwork suggesting export documents may have been falsified, flouting strict national and international laws designed to protect countries from importing diseased animals.

We've also uncovered evidence that one of Australia's biggest exporters may be breaching the system set up just three years ago to protect Australian animals overseas.

The Australian Department of Agriculture is now investigating these allegations and has formally requested 7.30 hand over evidence obtained for this story.

Matt Peacock has this exclusive report, which contains some confronting images

MATT PEACOCK, REPORTER: Once again this month, Australian livestock is being transported to Bahrain and Egypt, following long suspensions of a trade that's been dogged by controversy.

But now 7.30 has uncovered possible criminal conduct at the heart of the industry. There is evidence to suggest that key export documents have been falsified.

MELISSA PARKE, LABOR MP FOR FREMANTLE: Well I think that if there has been doctoring of any documents, then the full force of the law should be brought to bear on that. That's criminal action.

MATT PEACOCK: After the trade to Indonesia was suspended three years ago, new rules called the Exporter Supply Chain Assurance System, or ESCAS, were introduced, which hold exporters responsible for animal welfare all the way from the farm through to an approved abattoir overseas.

BARNABY JOYCE, MINISTER FOR AGRICULTURE: This system tries to balance the needs of having a trade that brings a fair return back to Australian farmers and the desire by the Australian people to have animals treated humanely.

MATT PEACOCK: But 7.30 can reveal a major breakdown in the system, with possible breaches of the law and claims by animal welfare advocates that a Perth-based exporter, Livestock Shipping Services, or LSS, is flouting the rules, leading to ongoing cruelty against Australian animals.

It's here in this office in a quiet suburban backstreet in Perth that LSS is based and I've been trying to get an interview with its live export manager, Gary Robinson - so far, to no avail. But Mr Robinson has expressed in other media interviews his contempt for the ESCAS process.

GARY ROBINSON, GM, LIVESTOCK SHIPPING SERVICES (ABC Radio, 15 Oct. 2013): It's failing exporters because exporters can't operate their business properly. It's failing producers because producers are receiving half the price that they should be receiving for their livestock. It's failing our customers because they are offended that the Australian Government wants to apply these rules on them.

MATT PEACOCK: Gary Robinson is no stranger to controversy. 18 months ago, he was Middle East manager for another major exporter, Wellard, and was involved in one of the most infamous incidents in the history of the live export trade.

Wellard's ship, the Ocean Drover, was refused permission to unload in Bahrain after authorities there declared the sheep onboard were diseased. It was a claim that was later disproven. Wellard diverted its shipment to Pakistan. But once the Pakistan Government realised Bahrain had rejected the shipment, it moved in to conduct a brutal cull.

Pakistan, on that trip, I remember you stated afterwards that it was horrible, that it was appalling to see.

MAURO BALZARINI, CEO, WELLARD: One of the worst thing in my life, definitely. It was touching for me as well. Very - I took it very personally.

MATT PEACOCK: 7.30 has now discovered that the documents used to gain permission to land the sheep in Pakistan appear to have been falsified.

Each export shipment needs a Certificate of Australian Origin, in Perth, issued here at the Fremantle Chamber of Commerce. Certificates have a series of stamps and signatures to prove their authenticity.

The problem is that we've got this document which, unlike your stamp, it doesn't have the date below it. And also up here, it's a written number, but you do what? You put a stamp on that, don't you?

VICTORIA WILLETTS, FREMANTLE CHAMBER OF COMMERCE: We do, yes.

MATT PEACOCK: According to the Chamber of Commerce, the certificate was never authorised.

So that's a stamp there, compared to this where it's just been written in. Do you ever do that?

VICTORIA WILLETTS: No, we don't. We're not allowed to.

MATT PEACOCK: Pakistan's Government also issued this No Objections Certificate, or NOC, listing the health requirements for the ship to land. But a copy of the same certificate required to be lodged with the Australian department had a key phrase - "if for breeding" - inserted. The sheep weren't for breeding, they were for slaughter. The effect of this amendment was that the exporter had no need to prove it had met all of Pakistan's health requirements.

MATT PEACOCK: Have you seen this?

MAURO BALZARINI: Yes, I've seen that and it's a very complex matter.

MATT PEACOCK: The CEO of Wellard was so concerned when he saw the documents, he reported it to the police.

MAURO BALZARINI: As you know, Garry Robinson doesn't work for us anymore, so I don't think it's proper, maybe, to comment on him in this venue.

MATT PEACOCK: An email sent by Garry Robinson at the time obtained by 7.30 refers to, "... a copy of the certificate that has had magic done to it," and suggests, "... we do not want anybody to compare the magic with the original".

Your manager, Garry Robinson, again, wrote an email describing the "magic" that had been done to this document. He didn't want others to look at it because they might compare the "magic" with the original. That again does suggest falsification of figures.

MAURO BALZARINI: Yes, it does. And we only discovered that much after the event and we've taken the action that we had to take for that.

MATT PEACOCK: Which was what?

MAURO BALZARINI: It's the action that you take when you find that something has not been done in the proper way and that's it.

MATT PEACOCK: In another email, Robinson notes that 601 sheep were missing. To avoid an automatic government inquiry, he urged colleagues to doctor the numbers, saying, "We'll need to add the 601 heads discrepancy to slaughter figures so there are not 601 heads missing."

Again, that appears to be falsification of figures.

MAURO BALZARINI: Yeah, is probably - you're probably right. It was not behaving in the right manner and that's why I tell you before that when we found out all this, we did what we did.

MATT PEACOCK: I mean, if this is proven, these are criminal acts.

MAURO BALZARINI: I'm not a policeman, unfortunately. I can only say that when you run a company, you've got certain responsibility and I am pretty sure I've done what a responsible head of a company like Wellard would have done in that case.

MATT PEACOCK: Mind you, when these actions happened, they were under your name, under your company's authority. Have you reported this to the authorities?

MAURO BALZARINI: We did report the - we reported what we found that - what we thought was wrong.

MATT PEACOCK: And has there been any follow-up action since that you're aware of?

MAURO BALZARINI: I cannot talk about that.

MATT PEACOCK: Why not?

MAURO BALZARINI: Because not - because there is confidentialities that I need to respect.

MATT PEACOCK: OK.

18 months later, Mr Robinson has left Wellard for LSS, where he's general manager. And it's LSS, particularly in Gaza, that critics are increasingly accusing of breaching the Australian animal welfare system.

SHATHA HAMADE, LAWYER, ANIMALS AUSTRALIA: The breaches, the recurring breaches and the horrific, sickening cruelty that we have documented in Jordan the first, second, third time, in Gaza, in October last year, and again in February this year, are supply chains that are owned and operated by LSS.

MATT PEACOCK: This footage, first posted on YouTube, but some shot as recently as last week, shows animals being slaughtered outside Australian-approved facilities.

MAURO BALZARINI: Those videos and those pictures should never come up and I hope that in the future, everybody will do the right thing so that they will not come up again.

MATT PEACOCK: Action should be taken?

MAURO BALZARINI: Action should be taken, yes, I think so, yeah.

BARNABY JOYCE: If the exporter's not doing their job, we will manage them, and if we have to manage them to such an extent as they don't get access to cattle again, then that's what we'll do.

MATT PEACOCK: In a statement, LSS says it's now voluntarily suspended exports to Gaza, deployed additional staff and is making a concerted effort to reconcile livestock numbers.

The department is now investigating the evidence of possible false documents made available to it by 7.30, describing it as "serious allegations" of criminal offences.

BARNABY JOYCE: It's a criminal act if it's forged. And people who break and breach the Crimes Act will get themselves a criminal conviction, and if it's serious enough, they'll get themselves a stint at Her Majesty's pleasure. So, you can't forge documents and think that you're going to get away with. If they're proven to be forged, you're in real strife.

SARAH FERGUSON: Matt Peacock with that report.

Former Wellard manager Garry Robinson declined our requests for an interview, saying he is restrained by commercial confidentiality.

You can also look at some of the documents behind this story, such as an authentic Certificate of Australian Origin document bearing correct stamps, compared with a certificate of Australian Origin for Pakistan with handwritten entry and dateless stamp, an email referring to 'magic' done, and an email from Garry Robinson on sheep figures.

We also have a media statement from Livestock Shipping Services.