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.