Agriculture Minister David Littleproud has launched an extraordinary review of his department after shocking revelations of cruelty to sheep revived calls for Australia's live export trade to end.
The industry is under pressure after whistleblower video footage emerged showing dozens of distressed sheep struggling to breathe while dead animals are thrown over the side of the boat in August 2017.
Mr Littleproud announced an audit of the Agriculture Department's capability, powers and culture, saying the independent regulator needed the right tools to ensure exporters do the right thing.
He said the department's report into last year's voyage had not matched the footage exposing cruelty onboard the ship where about 2400 sheep died after leaving from Fremantle.
"That is quite disappointing to me. I have some real difficulty around that," he told reporters in Melbourne on Monday.
The Emanuel Exports ship will have to satisfy authorities it's made improvements before it is allowed to set sail on its next trip to the Middle East after concerns about the airflow in sheep pens.
Australian Maritime Safety Authority inspectors visited the MV Awassi Express on Sunday and were concerned about the airflow over some pens.
"AMSA has advised the master and ship operator that they will have to arrange a third party airflow verification report to prove compliance with air flow standards before an Australian Certificate for the Carriage of Livestock can be issued," a spokesperson told AAP on Monday.
Mr Littleproud praised the person who exposed the cruelty and said a new whistleblower hotline would be established by the end of the week.
He also foreshadowed bigger fines and possible jail time for company directors, in addition to measure in a bill before parliament which doubles existing penalties.
"I'm horrified and shocked by what I saw and I know every Australian is horrified by those images of cruelty to sheep," Mr Littleproud said.
But he resisted calls from political opponents for a renewed ban on live exports, saying that would punish farmers and exporters who had done nothing wrong.
Animals Australia and the RSPCA are adamant the industry should be shut down.
"There is every reason to believe that what we saw on those five voyages last night is typical of what occurs on every voyage that takes place from Australia's shores," RSPCA chairman Gary Humphries told reporters in Canberra.
About 200 protesters gathered outside the West Perth offices of Emanuel Exports on Monday, chanting "save our sheep" and "get the sheep off the ships".
Western Australia's Agriculture Minister Alannah MacTiernan called for a summer ban on livestock exports and older live export ships to be phased out.
The Agriculture Department says it will add an independent department veterinarian to the upcoming voyage to the Middle East.