The Australian agriculture minister, David Littleproud, has launched an urgent investigation in the department of agriculture over livestock deaths on a live export ship, saying conditions on the ship were “bullshit.”

About 2,400 sheep died on an Emanuel Exports ship from Fremantle to the Middle East in August 2017, mostly from heat stress. A whistleblower filmed conditions on the ship and provided the footage to Animals Australia, which showed it to Littleproud on Wednesday.

He said the footage showed dead and decaying sheep.

“I saw footage provided to me by Animals Australia, which is very disturbing,” Littleproud said. “I am shocked and gutted.

“This is the livelihood of Australian farmers that are on that ship ... This is their pride and joy and this is total bullshit that what I saw has taken place.”

The ship left Fremantle on 1 August carrying 63,804 sheep bound for Qatar, Kuwait and the United Arab Emirates. It was subject to the standard investigation by the federal environment department because the number of sheep killed by heat stress pushed the mortality rate to 3.76%.

All live export shipments with mortality rates of more than 2% are subject to review.

Littleproud said he had already demanded an explanation from the department after receiving the report into this incident on 29 March, before being made aware of the Animals Australia footage.

“There was an unacceptable fatality rate because of a heat event,” he said. “I asked for further information. I also wrote to the live export industry.”

In a statement on Thursday, Littleproud said he had an urgent meeting with the department since viewing the footage and thanked Animals Australia – an organisation that has previously been in conflict with federal agriculture ministers – for sharing the footage.

“I’m shocked and deeply disturbed by the vision,” the statement said. “I thank Animals Australia for bringing this to my attention.

“We need to create an environment where groups, whistleblowers and individuals are comfortable and confident coming forward so we can nail those who do the wrong thing.”

It is not the first time Emanuel has suffered a mass mortality event due to heat stress on one of its live export ship, which is a converted car carrier.

While the shipment detailed in this incident was on route last year, the Perth-based exporters were warned of possible prosecution over a shipment in July 2016 on which 3,027 of the 69,322 sheep onboard died, leaving a mortality rate of 4.36%.

A report on that shipment said there were so many dead sheep that it was difficult to manage the bodies.

According to the department’s mortality investigation into the August 2017 shipment, temperatures in the gulf reached 36C with 95% humidity overnight, noting that under those conditions “large number of animals will start to die.”

It said that Emanuel rostered on extra crew to “undertake additional housekeeping” and keep water troughs full. They also opened “excessively boggy pens and those in hotter areas” to allow sheep to spread into the alleyways.

“These actions however, were insufficient to prevent the reportable mortality incident,” it said.

The department said it required Emanuel to follow a heat stress management plan for their next shipment, which took place in September and had a mortality rate of 0.52%.

The department said in 2017 that it would review its heat stress policies in time for the 2018 Middle Eastern summer.

Littleproud said he had demanded an update of that review.

“I will not be afraid to call out and take strong action against those who have not fulfilled their responsibilities, whether they be the exporter, the regulator or staff on ships,” he said. “I support the farmers who rely on live export and the exporters who do the right thing … Farmers care for their animals and they’ll be angry and hurt when they see this footage.”

Animals Australia said they had contacted Littleproud on behalf of the whistleblower, who had provided the footage to 60 Minutes.

“This announcement by the minister speaks to the seriousness of this situation and the strength of the evidence provided to the Government,” a spokeswoman for Animals Australia said.