There is doubt over claims that a small percentage of an Australian sheep shipment originally destined for slaughter in Bahrain have the viral disease scabby mouth.
Last month the Ocean Drover, carrying 21,000 sheep, was blocked from unloading in Bahrain.
After being stranded at sea for more than a week, the ship was diverted to the Pakistani port city of Karachi and cleared for unloading.
The Pakistani Secretary for Livestock says all the sheep need to be destroyed as scabby mouth could endanger other animals and human health.
But the Pakistani Meat Exporters Association says the testing process was flawed and the animals are healthy.
Australia's Federal Agriculture Minister Joe Ludwig said on Tuesday night the culling had been halted, the ABC reported. He had little detail.