63,000 sheep were being exported from Perth to the Middle East when 2400 died from heat.

The Australian government says it will investigate the deaths of thousands of livestock during transit to the Middle East, after being supplied with footage of decaying sheep by Animals Australia.

Federal Agriculture Minister David Littleproud said that what occurred was just "total bulls..t" and "disgusting" and has asked for the shipping company's practices on the August 2017 export to be thoroughly examined.

He said 63,000 sheep were being exported from Perth to the Middle East and, although there was a vet on board the ship, 2400 died because of a heat event.

A report was submitted by the shipping company last Thursday and the minister requested further information when he saw the fatality rate and research about "high heat mortalities".

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However, on Wednesday, footage taken during the export of the sheep was supplied to his office.

These included two four-minute videos which depicted dead and decaying sheep, he said.

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

"I saw footage provided to me by Animals Australia which is very disturbing. 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," he added.

He thanked Animals Australia for acting as a whistle blower.

Littleproud promised to take strong action against those who have not fulfilled their responsibilities, whether they be the exporter, the regulator or staff on ships.

"I support the farmers who rely on live export and the exporters who do the right thing. We need this trade for our farmers," he said.

"Farmers care for their animals and they'll be angry and hurt when they see this footage."

The Australian Livestock Exporters' Council says the footage is "highly distressing".

"These deaths and the conditions in which they occurred are plainly unacceptable," chief executive Simon Westaway said.