The consignment of sheep had become a major subject of controversy with even the Australian High Commissioner, Peter Heyward, intervening in the matter at one point.
However, the Sindh provincial authorities have started poisoning the 21,000 infected sheep after concluding that it was infected with salmonella and actinomyces bacteria.
The consignment was initially shipped to Bahrain by Australian company, Wellard Exports, but Bahrain rejected it after reportedly finding them infected with scabby mouth disease.
The sheep were than shipped to the Karachi Port Trust on September 5 by a local importer and the Sindh government provisionally cleared the consignment.
Sindh Livestock and Fisheries Secretary, Syed Abid Ali Shah, had also said the Australian sheep were not infected with any contagious bacteria and were healthy.
Even the Australian high commissioner to Pakistan said that the sheep had been inspected at the Karachi port and were cleared.
But Commissioner Karachi, Roshan Ali Sheikh, gave the orders for the elimination of the sheep through administration of poisonous injections after lab tests confirmed the infections.
Shaikh said that the process of killing and dumping the sheep has begun under the supervision of deputy commissioner of Karachi.
He added that officials from the federal and provincial governments along with the Karachi Metropolitan Corporation (KMC) are present on the site to oversee the process that might take a few days.
The commissioner said that the process was initiated on the directives of Livestock Department, as they said that the sheep were not "safe for human consumption."
Thousands of sheep are sacrificed by Pakistani Muslims during the festival of Eid-ul-Azha, which this year will fall in the last week of October.