Meat and Livestock Australia has rejected claims that it knew for years about the brutal treatment of livestock in Indonesian abattoirs.
Had MLA known about the "grotesque brutality" it would have acted, chairman Don Heatley said.
He denied MLA had admitted to knowing about the mistreatment of Australian cattle.
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"That is totally incorrect," he told ABC Television on Thursday.
Another senior MLA official, Michael Finucan, on Wednesday said the organisation had always known there were issues in Indonesia.
He said "resources and time and energy and effort" had been committed to being in Indonesia, but admitted MLA had always known there was more to do.
Mr Heatley said MLA was dealing with issues on a daily basis.
"We work across a whole range of areas from the feedlots to the processing sector to shipping," he said.
Australia was the only country in the world that invested in animal welfare outside its own borders and MLA had spent some $4 million in Indonesia to improve the system.
"If there was complete and utter knowledge of the brutality, the grotesque brutality that we saw recently, we would have been in there immediately," Mr Heatley said.
"We are talking about a rogue isolated incident of four abattoirs only and that should not be used to condemn the whole Indonesian market."
Mr Heatley said MLA operated in about 100 Indonesian abattoirs but now planned to confine its efforts to 25, including those highlighted in an ABC Four Corners report last week.
The federal government has suspended for six months live exports to Indonesia, but has yet to decide whether compensation will be paid to Australian graziers affected by the decision.
Mr Heatley said MLA had no plans to pay compensation to affected producers because it did not have sufficient reserves.
A Queensland University professor has suggested the industry knew as far back as 2005 there were problems in Indonesia.
Clive Phillips says the export organisation Livecorp asked him to submit a project researching slaughter practices at international abattoirs.
"The project that we submitted included evaluating the casting box shown in the Four Corners report and other aspects of the slaughter," he wrote on The Conversation on Thursday.
Professor Phillips, an animal welfare expert, says his project was rejected.
"The fact that Meat and Livestock Australia and LiveCorp were interested in commissioning research suggests that they were well aware of the conditions faced by animals in Indonesia long before these were exposed."
