Disturbing new footage has emerged showing what are believed to be Australian cattle being mistreated in Indonesian abattoirs.

The footage aired on ABC1's Lateline was shot in January in two abattoirs in Jakarta and shows workers slitting the throats of cattle without stunning them first and cutting animals up while still alive.

The Federal Department of Agriculture is investigating the vision to establish if the cattle are Australian and if the slaughterhouses are part of its approved abattoir system.

Last year, live cattle exports were banned for two months after Four Corners aired footage showing horrific treatment of cattle in Indonesian abattoirs.

When the Government resumed trade, it did so under strict new guidelines stating exporters must guarantee the welfare of all livestock that leave Australia.

But the latest video raises serious questions about the new regulations and the RSPCA says it has counted 46 potential breaches of the new rules.

The footage was shot by an Indonesian investigator engaged by Animals Australia, at Timur Petir and Cakung abattoirs.

It shows what animal welfare campaigners and cattle industry insiders believe to be an Australian Droughtmaster steers inside Australian-designed Mark 1 and Mark 4 restraint boxes.

Lyn White from Animals Australia has filmed in 11 abattoirs in Indonesia and her investigations led to last year's Four Corners program.

"This latest footage reveals that workers can't even be relied upon not to start cutting up Australian animals before they are dead," she said.

"My Indonesian contacts said that that animal had an Australian ear tag, the other factor is it's a Droughtmaster steer, which is a breed of animal that is being exported from WA to Indonesia."

'Distressing' footage

Footage was also obtained from Cakung abattoir, which has much lower standards than Timur Petir, and there are fears Australian cattle are ending up there as well.

At Cakung, local animals are slaughtered on the floor, while Mark 1 boxes are used for larger cattle.

RSPCA chief scientist Bidda Jones says the Mark 1 boxes are totally inappropriate for slaughter.

She has viewed over an hour's worth of footage from the two abattoirs which she describes as "distressing".

Dr Jones has identified 46 potential breaches of the Federal Government's new checklist set up to protect animals exported to foreign abattoirs.

"The kind of breaches that I saw in this footage were, for example, animals vocalising when they're in the box, and when they're restrained, water being used on the animals before they've been slaughtered, so that's distressing and shouldn't be allowed," she said.

"We'd see animals being slaughtered when the knife cut isn't a single, uninterrupted stroke, where the animals are being restrained for longer than 10 seconds, where the slaughtermen are not holding the head with the neck extended so the wound doesn't come into contact with the equipment.

"Where slaughtermen are interfering with the wound before they've confirmed that the animal is dead, and no confirmation of death in any of the cases that I looked at."

Sorry, this video has expired Lee Rhiannon talks to ABC News Breakfast

A spokeswoman for Agriculture Minister Joe Ludwig said the department was investigating complaints regarding three Indonesian abattoirs.

"The Government is implementing significant reforms to the live animal export trade. These include supply chain assurances that trace animals from port to slaughter house and make exporters responsible for their supply chain on a consignment by consignment basis," she said.

"The Department of Agriculture, Fisheries and Forestry has received a complaint regarding animal welfare in three Indonesian abattoirs.

"As the regulator, the secretary of the department will now investigate the matter. It is appropriate that we allow this process to be completed. Following the investigation, the regulator will take appropriate compliance action, if required."

Under the new regulatory framework for the live animal trade, exporters must audit abattoirs in Indonesia to make sure they meet Australian standards

But the Federal Government would not confirm whether the two Indonesian abattoirs seen in the latest footage are approved for Australian exports.

The Agriculture Department said it could not reveal the names of approved abattoirs for commercial reasons.

Ms White says the Government's response to the latest footage proves the new system is not working.

"Neither the industry or the Government will tell us what facilities have been accredited and that just shows they have something to hide, that they are not confident in this new system whatsoever," she said.

"Part of the Government's response to the expose of last year was saying that there'd be greater transparency. That's clearly not the case."

The Greens spokeswoman on animal welfare, Lee Rhiannon, says the practices aired on Lateline cannot be dismissed as isolated cases.

She says if the animals are confirmed to be Australian, the live export industry should be shut down.

And she says if the Federal Government is not brave enough to take that action it should impose sanctions on rogue producers.

"The Government should immediately stop these operators from exporting from Australia to Indonesia," she said.

"There does need to be sanctions that actually have repercussions for those operators who are not following through with the export supply chain."

She says the Australian Government has not done enough.

"We do need the monitoring and auditing in this area," she said.

"While the Greens will continue to call for an end to live exports we recognise there is an immediate need for the Government to deal with the situation and they need to apply the full force of sactions in the first instance."

Lateline understands Australian industry trainers have already been sent in to Timur Petir.