Already reeling from footage of Australian cattle being brutally slaughtered in Egypt, footage has emerged of goats being stuffed into sacks and put in the boot of a sedan in Malaysia.

In 2011 cruelty to Australian cattle in Indonesian abattoirs led to a month-long trade suspension and tough new rules for exporters. The rules require the whole supply chain, including abattoirs, to meet world standards with no sale or slaughter of animals outside of approved facilities.

The Malaysian footage, shot by Animals Australia activists, shows goats being sold outside of approved facilities for private slaughter. The investigation also documented cattle allegedly being killed in a substandard manner.

Malaysia accounted for 85 per cent of Australia's live goat exports in 2010-11. Last year more than 59,000 goats were exported there.

Critics of the industry, including many on Labor's backbench, say the recent revelations put the trade on a last warning and highlight the need for an independent office of animal welfare.

Official budget costings prepared for the Greens and seen by Fairfax Media show that setting up the office would cost $500,000. Labor's national conference and caucus have endorsed the idea but the government is yet to act.

Greens Senator Lee Rhiannon said the price tag was cost-neutral because the office would simply take the animal welfare officers from within the agriculture office and place them in a separate department. '

Animals Australia campaign director Lyn White said Agriculture Minister Joe Ludwig's recent claim that 99.9 per cent of Australia's exported animals had good animal welfare outcomes was ''at complete odds with the facts''.

''Not only are the majority of exported animals subjected to traumatic forms of restraint before having their throats cut whilst fully conscious, Animals Australia is consistently providing [the Department of Agriculture, Fisheries and Forestry] with evidence that required standards and regulations are being breached,'' Ms White said.

Live Exporters Council chief executive Alison Penfold said any allegation needed to be investigated. She said the system allowed problems to ''identify, isolate and fix issues when they arise rather than shutting down a whole trade''.

''We oppose all animal cruelty and Australia is the only country of 100 exporting nations that is investing in continuously improving global animal welfare through our training and investment in infrastructure in our destination markets,'' she said.