Agriculture Minister Joe Ludwig says he was appalled by the recent brutal slaughter of 21,000 Australian sheep by Pakistani authorities but says he is satisfied that all due diligence has been done for an upcoming export of live cows.

The minister was commenting on a report by the ABC's Four Corners on Monday, which probed the circumstances surrounding the inhumane culls in September and October.

Officials from the Sindh provincial government claimed the slaughter - which saw some sheep buried alive - was necessary due to health concerns, but these claims were vehemently rejected by Australia's live export industry and the Department of Agriculture, Fisheries and Forestry (DAFF).

Exporter Elders is now preparing to send a shipment of nearly 3000 breeder cows, 2000 of which were destined for Pakistan, where they would be under the supervision of the same government department that carried out the cull.

Senator Ludwig says he is satisfied that the department has done all of the due diligence for the export of the cows.

"Breeder cattle are are quite expensive animals to begin with," he told ABC Television on Monday.

"They are also likely to end up within local herds and well looked after - they have a long productive life."

He said he was disgusted by the scenes of the sheep being slaughtered in Pakistan.

"It was certainly appalling," the minister said.

"No one would have expected that - it was unprecedented.

But he stood by his department's handling of the case, saying the animals were not rejected on the basis of any health problems.

"The High Commissioner in Pakistan, myself, the department, everyone including the exporter and the importer did everything they could to ensure the animal welfare of those sheep," Senator Ludwig said.

"Ultimately, it didn't succeed (and) we had an appalling circumstance."

The department says it is investigating the case for any possible breaches of the Exporter Supply Chain Assurance System.

"We do not know the reasoning behind the Pakistan authority's decision to cull the sheep in Pakistan or their choice of the method used," DAFF said in a statement.

"We continue to hold that both the decision and the method used were unnecessary."

RSPCA Australia chief executive Heather Neil said the ABC report showed the live export trade wasn't worth the risk.

"No matter how much industry or government involvement there is, the live export of animals for slaughter presents an unacceptable level of risk for the animals and is inherently cruel," Ms Neil said.

AAP