The Department of Agriculture, Forestry and Fisheries (DAFF) issued permits last Monday for three exporters for 190,000 sheep and 400 cattle to be exported to the Middle East.
But WA Live Exporters Association (WALEA) chairman John Edwards said while the permits were welcomed it didn't mean the industry was exactly back on track.
"It is a shipment-by-shipment and a market-by-market scenario at the moment," Mr Edwards said.
The three companies with permits are believed to be Wellard Rural Exports, Emanuel Exports and Livestock Shipping Services.
Th go-ahead came amid reports that there were 300,000 sheep caught up on farms or in exporter feedlots as a result of the delays and that it would take a long time to work through the backlog.
Mr Edwards said it would take time for the industry to get back on its feet.
"While the permits are good news it doesn't alleviate the issue which is before industry for both producers and exporters," he said.
"There are large numbers of sheep on farms in export condition and numbers add to that position day-by-day as we move forward.
"Shipping approvals today (Monday) doesn't necessarily alleviate next month's problems in terms of a backlog building because it is all about shipping availability and vessels available.
"Only a fraction of those 300,000 sheep will get shifted over the next couple of months."
During the delay in shipments, Mr Edwards said animal welfare issues could have arisen on-farms as farmers, particularly in the Wheatbelt, waited for rain.
He said the Federal Government did not fully understand the impact stopping "a few live export boats" had on the entire industry.
"We need to start looking at the food security issues for a lot of these markets," he said.
"These markets are highly dependent on live Australian sheep.
"There are commercial and political concerns which need to be dealt with.
"We need a government that understands our industry far far better than it currently does and the difficultly of trading live animals or perishable products overseas."
Mr Edwards said the issue in the future would be trying to keep confidence in the sheep industry.
This was not only applied to farmers but also exporters as the companies dealt with government interference in commercial issues.
"It is about declining prices and the viability of the sheep industry after we have busted our backside for the last two years to try and encourage farmers back into sheep," he said.
"It is a confidence thing in the sheep industry now - for the whole industry."
In a statement DAFF said the approvals were granted only after exporting companies were able to assure it that additional animal health and welfare safeguards were in place.
It said exporters must now:
p provide more detail about what they would do if a shipment is delayed or refused unloading
p carry additional feed, water and veterinary supplies to cover the possibility of diversions and delays
p engage additional stock handlers
Wellard Rural Exports confirmed that it had received a permit from DAFF to export 65,000 sheep to Qatar.
Wellard managing director Mauro Balzarini said the company was disappointed with the delay in issuing the export permit and the view that everything that relates to sheep export was perceived as "risky".
"These sheep are bound for Qatar, a market which we have been supplying for almost 25 years without incident," he said.
"Qatar readily embraced the Exporter Supply Chain Assurance System (ESCAS) and has adhered to the Memorandum of Understanding (MOU) when tested successfully in the past.
"Nevertheless, Wellard has worked with DAFF to achieve a solution to this impasse and to allow live exports to continue to provide an important marketing option for Australian farmers and to provide consumers in the Middle East with a safe, healthy, sustainable supply of fresh meat."
Emanuel Exports managing director Graham Daws said he was disappointed in how the Federal Government had handled the whole process.
Mr Daws said it took far too long to issue the permits and cost exporters tens of thousands of dollars.
In addition he said the new conditions would not impact on the condition of the animals.
"There is already a comprehensive and rigorous system with animals from the start to the finish in place," Mr Daws said.
"Having additional conditions imposed just shows that the regulator really doesn't seem to have any faith in their system, even though we know it is working satisfactorily."
Mr Daws said the fact Kuwait had processed the sheep which had been diverted from Bahrain showed it was an over-reaction to the publicity surrounding what had happened.
"The prolonged delay for issuing permits has rocked the confidence of importers as to whether Australia is really serious about the continuity of this business and whether it can be relied upon in the future," he said.
Rumours that prices for sheep contracts signed prior to the delay had been lowered were refuted by Mr Daws.
He said he couldn't speak on behalf of the whole industry but believed all existing contracts would have been honoured.
But he admitted anything which was purchased from now on would be at current market value which was far below the previous contract prices.
"If this industry does not have continuity there will be a collapse in price like we have just seen and it will get even worse when the spring lambs come along," he said.