A live export company has released grisly footage of Australian sheep being brutally slaughtered in Pakistani feedlots, in advance of a Four Corners special aired tonight.

A shipload of 21,000 Australian sheep was sent to the Pakistani port city of Karachi after being refused permission to be landed in Bahrain because of disease concerns.

On September 16, Pakistan's federal government ordered the local authorities in Karachi to destroy the sheep.

Officials from the Sindh Livestock Department, supported by heavily armed police, moved in.

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Four Corners has footage of a man sawing at a sheep's neck before throwing it into a bloody pit.

Angered by what was happening, some local PK Livestock staff recorded vision on their mobile phones.

The industry has moved to pre-empt the story by releasing a video statement on YouTube, including its own vision of the sheep being killed.

The video features Steven Meerwald, from Wellard, the company responsible for the shipment.

"By now you will be aware of the incident in which livestock authorities in Pakistan culled more than 20,000 sheep Wellard had exported from Australia," Mr Meerwald says in the video.

"I've just spent six weeks in Pakistan fighting for the right to humanely process the sheep according to the appropriate international standards.

"You're about to see some of what took place in Pakistan. This occurred after our people were forcibly removed from caring for these sheep.

"We immediately informed the Australian Government about what was happening and have been very public in our condemnation of the treatment from the day it occurred."

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The company saw the vision of the sheep being killed more than a month ago.

The sheep were never supposed to go to Pakistan. They only ended up there after authorities in Bahrain rejected the shipment, claiming the animals were infected with scabby mouth.

Despite a legal challenge, and high level government, diplomatic, scientific and industry representation, the cull still took place.

Australia's Department of Agriculture says it was powerless to stop the slaughter.

Australia's live export industry was given strict new rules after the Indonesian live cattle export trade was suspended, and then re-opened, in the wake of another Four Corners report.

Under the new rules, Australian sheep and cattle have to go through approved supply chains which meet international welfare standards.

Now the Federal Department of Agriculture, which ticks off on the supply chains, is once again facing questions about how, or if, animal welfare in the live export trade can be guaranteed.

Philip Glyde is deputy secretary at the Department of Agriculture and spoke with Four Corners reporter Sarah Ferguson.

Sarah Ferguson: "In spite of all of those efforts by the Australian Government, the cull continued." Philip Glyde: "Correct." SF: "You were ignored." PG: "Um, that's the outcome. That despite the efforts of all, from the very senior levels of government down, we were not able to prevent the cull continuing, and so 21,000 sheep were euthanased." SF: "Euthanase is not an apt word to describe what happened there." PG: "Fair comment."

The live export industry is hoping the Pakistani case does not overshadow what it says is the good work improving the trade.

"Big reform is never easy and it takes time to get it right," Alison Penfold, from the Australian Livestock Exporters' Council, said.

"But we have seen progress with exports, with the exporter supply chain assurance system, and the one thing that that system allows us to do like never before is where an issue arises in a supply chain, we can identify, isolate and fix it."