The testing comes after Indonesia paused exports from four Australian facilities after a small number of exported cattle were detected with the highly infectious disease.
Australia's chief vet Mark Schipp has reassured Indonesian authorities that Australia remains free of the potentially deadly viral disease.
"We've never found evidence of lumpy skin disease in cattle that have been exported from Australia," he told AAP on Monday.
"Given the presence of LSD in Indonesia, positive results in cattle post arrival in Indonesia are not unexpected."
Authorities believe the cattle were infected either on the boat on the way to Indonesia or while they were in Indonesia, Dr Schipp added.
The disease can be spread by contaminated equipment and biting insects, like flies and mosquitos.
"Today we've collected samples from those four export yards that have been suspended by Indonesia ... and once we have those results we will convey those back to Indonesia," Dr Schipp said.
The test results for a total of 260 cattle, at two sites in the Northern Territory, one in Queensland and one in Western Australia, should be ready by Thursday.
The federal government has briefed state and territory ministers and had meetings with Australia's ambassador to Indonesia and other departmental officers.
"We have never had a positive detection on our shores," Federal Agriculture Minister Murray Watt said in a statement.
"Australian officials are working with Indonesian authorities to reassure them that all animals exported from Australia comply with all Indonesian requirements."
Senator Watt and Dr Schipp are due to answer questions from stakeholders at a public meeting on Monday night.
Australian producers and the beef supply chain can be assured the government is working to resolve the issue, Senator Watt added.
Nationals Leader David Littleproud urged "calm and understanding."
"I think we'll demonstrate that Australia doesn't have lumpy skin," he told Sky news on Monday.
"I'm confident that this didn't start in Australia, that in fact it was in Indonesia, but the Indonesians have rightly asked for us to demonstrate that."
The Red Meat Advisory Council and National Farmers Federation have issued a joint statement, saying the Australian cattle were found to have Lumpy Skin Disease only after they spent time in Indonesia.
"The robust systems that Australia has for the ongoing monitoring of our animal disease status supports us to trade around the world," council chairman John McKillop said.
Australian livestock products continue to be traded, including live cattle to Indonesia, federation president Fiona Simson said.
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