Gillard used her meeting with her Pakistani counterpart Raja Pervaiz Ashraf during the Asia-Europe Summit here to tell him that Australians were distressed by "these acts of cruelty" and that she wanted the matter probed.
As many as 21,000 sheep were culled in Pakistan in September after livestock officials felt they were not fit for human consumption despite assurances from Australian diplomats that the animals were safe.
"This was a false claim about disease in these sheep and the industry has already voluntarily responded by suspending live sheep being sent to Bahrain and Pakistan," she said.
"(I was) very strong in raising those concerns and very clear this is something that has distressed the Australian people," she added.
Gillard was also quoted as saying that Australian government had been "working hard" to ensure that live exports was a sustainable industry with appropriate standards for animal welfare.
The entire shipment of sheep had been turned away from Bahrain after authorities said the flock of 28,600 carried disease.
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When they arrived in Karachi, authorities there also claimed testing showed the sheep were contaminated and ordered the destruction of the animals, an ABC report said.
A court order halted the cull after the deaths of 7,600 sheep and an independent test carried out in Britain showed the flock to be disease-free, the report said.
But Karachi authorities rejected these tests and resumed the cull.
All 21,000 sheep have now been killed, and concerns were raised in Australia that the animals had been treated brutally.