The shocking footage, filmed by a navigation officer, shows dozens of sheep struggling to breath while dead animals are thrown overboard.
The officer told Nine Network's 60 Minutes that crew members fainted, while the sheep were essentially 'in an oven.'
Some of the footage, shown on the program on Sunday night, allegedly came from a voyage by market giant Emanuel Experts, which became the focus of the current affairs program.
Agriculture Minister David Littleproud told the Today Show the footage 'shocked me to the core' but he could not guarantee another ship that failed an inspection was set to leave Australia.
He said, 'This is outside my realm. Unfortunately the department who is the independent regulator gets to make the determination and I’m asking serious questions about making sure there is enough comfort around any further shipment going out.'
'The ship I understand is at Fremantle. There are around 50,000 sheep waiting to be boarded on to that ship once approvals have been granted, but approvals have not been granted at this stage.'
Today host Karl Stefanovic frustratingly said the footage was 'disgraceful' and an 'embarrassment.'
He then said the people responsible for the cruelty should be 'run out of town.'
Mr Littleproud responded: 'Karl, I’ve been Minister for three months. This is the first one of these incidents I have had.
'I intend to make sure we are a fair country, everybody gets a fair go, but the reality is as I said earlier, if standards haven’t been breached here today, then really the standards aren’t good enough.
'If they are not, I intend to work collaboratively. I’m meeting with Animals Australia and the RSPCA and the industry today to get a way forward.'