An Australian live export ship broke down en route to Jordan but is back on course after repairs, with the company saying the animals on board did not suffer adverse conditions.

The MV Ocean Drover, owned and operated by Fremantle-based Wellard, said on-board engineers fixed the main engine malfunction.

The 12-year-old vessel was stopped for 72 hours near the Cocos Islands while repairs and testing were carried out, the company said in a statement.

"Importantly, the provision of feed, water and ventilation to the 42,000 sheep and 6000 cattle on board the vessel were unaffected by the mechanical issues due to the redundancy provisions built into the ship to protect and enhance animal welfare," Wellard said.

The company said daytime temperatures as the vessel made its way to the Aqaba Gulf were averaging 27 degrees, "well below the 35-40 degrees the livestock experienced in their paddocks before being transferred to the vessel".

Wellard has notified both the Australian Maritime Safety Authority and the Department of Agriculture.

The company hit headlines in October 2012 when activists made death threats to staff after video footage emerged of its sheep being inhumanely slaughtered in Pakistan.

AAP