Witnesses to the culling of some of the 21,000 Australian sheep rejected by Bahrain and Pakistan described the process as inhumane and brutal. The Karachi edition of The International News cited a video which showed the animals being clubbed, stabbed and buried alive.

The video was taken with a mobile phone camera which explained why it was shaky.

The exporter of the sheep, Wellard, confirmed having seen the film of the brutal and unacceptable manner the flock was culled. However, they did not see the actual carnage since the Wellard staff was forced off the feedlot in Razzaqabad in Karachi.

"Like a giant mass of wool, bloodied and filthy, they lay in trenches - slit open, stabbed or clubbed to death, while many still wriggled with some life left in them, soon to be buried alive," The International News quoted the report by M. Waqar Bhatti.

"The people killing the animal or throwing them into the trenches were not wearing any protective gear whatsoever, even though the animals were being culled on the basis that they were suffering from a contagious disease," the report said.

Another report by the journalist Kazim Alam described the aftermath of the culling process.

"The culling process was halted but I could see that there was this lonely workers of the municipal authority, he was levelling the ground with a tractor, with a huge gigantic machine and he was levelling the ground," ABC quoted Mr Alam.

"Along the boundary of the pen I could see the dead sheep with flies buzzing around and it was really, really stinking," Mr Alam added.

Initial reports said the animals had salmonella bacteria, but an independent laboratory said otherwise.

Because of the controversy generated by the shipment of the 21,000 sheep, there are calls for the phase out and prohibition of the live sheep trade. Another industry group proposed that Aussie exporters focus instead on four Middle Eastern markets which had not rejected previous shipments of the animal to their countries.

PK Livestock, the importer of the sheep, secured a court injunction against the killing and a Pakistani high court order staying the cull order. Wellard Managing Director Stephen Meerwald said the culling was done outside strict new animal welfare benchmarks.

"I have watched the video and let me tell you that since I have seen those gruesome visuals, I haven't eaten or slept. Regardless of whether they were healthy or not, the way they were killed or buried alive is neither humane or Islamic," Mr Meerwald said.

Australia's Agriculture Department said it will investigate the report that the sheep were culled outside approved channels.

Animals Australia Campaign Director Lyn White said what happened in Pakistan is proof that live animal import has unacceptable risks.

"What Australian sheep have endured in Pakistan is unforgivable but the reality is that the only way to ensure such a terrible situation is never repeated is to end our participation in this cruel and unnecessary trade," AAP quoted Ms White.