Australia’s agriculture minister has announced a whistleblower hotline to expose cruelty on live export ships and will review the “skills and capabilities and culture” of his own department in response to shocking footage released on Sunday.

David Littleproud said he would also look at strengthening the penalties for live exporters who breached animal welfare standards so that company directors could face fines or even jail time.

The footage, filmed by the trainee navigator Faisal Ullah and released through the advocacy group Animals Australia to air on Channel Nine’s 60 Minutes on Sunday, showed sheep on five voyages to the Middle East during the 2017 northern hemisphere summer, including one trip on which 2,400 sheep died of heat stress.

Protesters were at Fremantle port in Western Australia on Monday, where the Awassi, the ship featured in that footage, was waiting for clearance to take about 55,000 sheep to the Middle East on Tuesday.

Disgust in Perth after footage surfaces showing shocking treatment of sheep on board a ship from WA to Middle East. @Rob7Scott pic.twitter.com/6a9T8c89Gg — Rob Scott (@Rob7Scott) April 9, 2018

Littleproud said the routine reportable mortality investigation conducted by the Department of Agriculture into the voyage had been inadequate in that it did not show many of the issues raised in the video.

“Quite candidly, that vision does not marry up with the report I have received and that is quite disappointing to me, to the extent that I have difficulty around it,” he said.

He said he had asked the attorney general’s office to help undertake a review of the “skills and capabilities and culture of the regulator” to ensure that investigations were more thorough in future, adding: “I am somewhat concerned that we have had to do this, but we cannot take at backward step.”

The whistleblower hotline is due to be established by the end of the week, with the help of Animals Australia and the RSPCA. It’s an uncharacteristic partnership for the federal agriculture minister’s office, which has previously had a more combative relationship with animal welfare groups.

Littleproud also suggested that penalties imposed upon exporters had been too light in the past and said he had consulted with Labor’s agriculture spokesman, Joel Fitzgibbon, to more than double existing penalties and target penalties at the heads of live export companies, rather than the companies themselves.

Western Australia’s live export minister, Alannah MacTiernan, has also called for tougher penalties on live exporters and accused the federal agriculture department of having “whitewashed” the mortality report on the Awassi’s August 2017 voyage.

MacTiernan said anyone who claimed to be “shocked” about footage from the Awassi “had their head in the sand”.

Quick Guide Live exports Show • The Australian live export trade grew rapidly in the 1970s to meet growing demand in the Middle East. • Australia exported 1.7m sheep in 2017 — the lowest number since records began in 1985. • About 80% were processed through Fremantle in Western Australia. • The mortality rate in 2017 was 0.9%, or 12,377 sheep. The average mortality rate has been trending down from a high of 1.75% in 1995. • Sheep are exported to Kuwait (36%), Qatar (30%), UAE (9%), Israel, Jordan, Lebanon, Oman, Singapore, Malaysia, and parts of northeast Asia. • Australia exported about 890,000 cattle in 2017 with a mortality rate of 0.1%. Cattle are exported to Asia, the Middle East, Northern Africa, Europe, and Mexico. • The Australian Live Export Council says the trade is worth $250m annually, but the 2016 National Livestock Export Industry Sheep, Cattle and Goat Transport Performance Report said the total economic value of the trade was $1.6bn.

“I’m not sure what they thought 2,500 or 3,000 sheep dying of heat stress in a confined space was going to look like,” she told reporters in Perth. “It was always going to look like this.”

MacTiernan said WA’s Department of Agriculture was investigating the shipment, consigned by the Perth-based exporter Emanuel Exports, for what she alleged were breaches of the state’s Animal Welfare Act.

She also called for a potential three-month ban of exports out of Fremantle, which processes 80% of Australia’s sheep live export trade, during the Middle Eastern summer.

An attempt in 2008 to charge Emanuel Exports under the Animal Welfare Act resulted in an acquittal in a Perth magistrates court because the magistrate found that while there had been animal cruelty as defined in the act, the state legislation was superseded by the federal legislation, including the live export standards that allowed the trade to continue.

MacTiernan said she was optimistic about Littleproud’s commitment but added that that the federal regulator could not be relied upon to act.

“Less than two weeks ago the federal government produced a report that basically whitewashed what happened on that vessel – which was an exact replica of what had happened a year before where they also had whitewashed it,” she said.

“The federal government has continued to allow companies that have offended to just go and do it again.”

Emanuel Exports was contacted for comment but declined to answer Guardian Australia’s questions.