Bahrain rejected the unloading of 22,000 sheep from a Wellard vessel forcing the exporter to unload in Pakistan.
And in the same week, 50,000 sheep on the Al Shuwaikh, run by Emanuel Exports, were also destined for Bahrain but had to be sent to Kuwait.
Both shipments were rejected due to the Bahrain Government raising concerns over incidences of scabby mouth disease.
Scabby mouth was not previously notified by Bahrain as a disease of concern and was a minor viral disease present in most sheep and goat flocks throughout the world.
Kuwait and Bahrain were part of the Tranche 1 implementation of the Exporter Supply Chain Assurance Scheme (ESCAS).
After Farm Weekly had gone to press last week, Wellard Rural Exports issued a statement saying the sheep were unloaded in Pakistan.
This week Wellard managing director Steve Meerwald said issues were still being dealt with.
"From an Australian perspective it worked well and now the sheep are in Pakistan," Mr Meerwald said.
"We are working as a collective to get the best result for everybody."
Mr Meerwald said Wellard did not have a shipment due to go to Bahrain any time soon and he doubted whether other exporters would take the risk until there was some clarity over what is accepted.
"And it isn't really up to the industry to sort out, it is a political issue and up to the Australian Government and Bahrain Government," he said.
Mr Meerwald was part of a group of exporters that met with Federal Agriculture Minister Joe Ludwig when he was in Perth last week.
He said he had raised the issue with Mr Ludwig and the Minister had agreed it was more than just a commercial issue.
"Until there is clarity and everybody understands (what is accepted) and there is confidence that exporters can discharge into that market then I think from a regulatory point of view exporters won't be taking that chance," he said.
Farm Weekly understands planned shipments to Kuwait are also on hold at the moment while the Federal Government seeks assurances from the Kuwait Government that Australian sheep would be accepted into the market upon arrival.
Emanuel Exports planned to have a vessel leave Fremantle on September 19-20 and had lodged paperwork but was still unsure if the Australian Government would approve that shipment to go.
Emanuels was waiting until government negotiations between Australia and Kuwait had been undertaken.
Mr Daws said the decision would come from the Australian Quarantine Inspection Service (AQIS).
Farm Weekly believes buying for the shipment has also been postponed until the go ahead is given.
WA Live Exporters Association (WALEA) chairman John Edwards said Kuwait was one of WA's first live export markets in the 1960s and the industry had never had any trade issues with the country.
"What is developing now is question marks surrounding the previous shipments and possibly questioning (Kuwait's) integrity in some respect in receiving Australian shipments," Mr Edwards said.
"And those sorts of things are not handled well by any customer let alone a long-time customer of Australian sheep which has stood by Australia through thick and thin.
"There is an MOU in place and they have a health protocol which has been in place between Australia and Kuwait for a long time.
"Now the Australian Government wants to question their own MOU in some respects when the Kuwaitis have agreed to the conditions and signed it."