Australian live cattle exports to three abattoirs in Vietnam have been suspended after footage emerged of animals being bludgeoned to death with sledgehammers.

Animals Australia secretly filmed the mistreatment of cattle at the abattoirs, revealing tied-up animals struggling to get away from men wielding sledgehammers.

The graphic footage shows at least five cows being bashed in the skull.

Agriculture Minister Barnaby Joyce said his department began investigating the mistreatment one day after the activist group handed over preliminary evidence.

The cattle industry has suspended all trade with the abattoirs but Mr Joyce insists exporters won't be dealt the blow suffered in 2011 when all live cattle exports were suspended to Indonesia.

Deputy Prime Minister Barnaby Joyce. (AAP)

"We will not be banning the live cattle trade," he told ABC TV on Thursday.

In a statement, he labelled the footage disturbing and "totally abhorrent".

"Anyone viewing this footage would be shocked and upset at the mistreatment and we are taking these reports very seriously," he said.

But despite Animals Australia claiming the cattle are Australian, Mr Joyce says their country of origin is not yet clear.

At least one of the abattoirs is not approved to slaughter Australian cattle.

Australian Livestock Exporters' Council chair Simon Crean said he would take "every step" to stop any exporter found to be breaching strict guidelines from supplying to Vietnam.

"I'm shattered. I mean, you look at that - it's inexcusable," he told ABC.

But he doesn't believe stopping Australian exports is the answer.

"Take Australia out of the market, that sledgehammering will continue," he said.

"I want to stop it, but you're only going to stop it with Australia in the trade."

Mr Crean admitted Animals Australia had brought similar evidence to the council before but was never given a response.

"That is a failing on our part," he said.

Animals Australia called for the department to be stripped of its regulator role, saying it was "hopelessly conflicted" with its duty to promote the live cattle trade.

"Nobody can claim they didn't know this was happening - the exporters knew, the department knew and the minister knew," Animal Australia's Lyn White said in a statement.

"Some exporters think they are above the law and they have good reason to."

Labor is accusing Mr Joyce of failing the live export sector with a "gung-ho, ask-no-questions approach" that left the regulatory regime struggling to keep pace with expansion into new markets.

"Events like this these will damage public confidence in live exports," opposition agriculture spokesman Joel Fitzgibbon said.

"It will take much work to re-build it."

Greens senator Lee Rhiannon is outraged by the footage, labelling the incidents "sickening, heart breaking and beyond belief".

She's calling on Prime Minister Malcolm Turnbull to intervene and strip regulatory powers from the department.