The measure will begin on Thursday, two days after Indonesian authorities confirmed the livestock disease was detected in the popular holiday destination of Bali.

“Starting tomorrow when flights arrive from Indonesia a biosecurity officer will board the aircraft on arrival and play a message, targeted at our concerns around FMD,” Australia’s chief vet Mark Schipp told AAP.

“One hundred per cent of travellers arriving from Indonesia will now be assessed against biosecurity risk profiles and receive some form of intervention. That might be they have their luggage X-rayed, they might be interviewed by a biosecurity officer.”

Dr Schipp said the virus’s spread to Bali was not unexpected but disappointing.

Other measures include detector dogs at Darwin and Cairns airports, and foot dips are being considered for passengers entering Australia.

But Dr Schipp said there were issues to work through regarding foot dips because of the chemicals used.

“They are very potent chemicals. You can’t get them on your skin, and a lot of passengers coming back from Bali, for example, are not wearing boots.”

Dr Schipp was hopeful the announced measures would stop FMD reaching Australia.

“I believe we will be able to keep it out well into the future … if we were to get an incursion it would have devastating consequences for Australian agriculture and for that reason we need to treat it very, very seriously.”

It’s estimated FMD would cost the Australian livestock industry $80 billion if it arrived in the country.

Dr Schipp said farmers would be compensated if the disease arrived here.

Federal Agriculture Minister Murray Watt said on Wednesday that biosecurity had already been ramped up at major airports servicing travel from Indonesia after the disease was detected on the archipelago in May.

All flights from Indonesia have operated with biosecurity profiles flagging higher-risk passengers for screening.

“Australian biosecurity and particularly the threat posed by FMD is a top priority,” Senator Watt said in a statement.

“High-level discussions have been occurring on an ongoing basis between Australian and Indonesian authorities as well as with local industry.”

National Farmers Federation president Fiona Simson welcomed the new biosecurity measures.

“Ever since FMD was detected in Bali our industry has been on edge given the growing volumes of traffic between our countries,” she said.

“We are relieved to see the government respond to calls by industry to ramp up biosecurity through detector dogs, greater communications material for travellers and further biosecurity staff training.”

The disease affects cattle, sheep, goats and pigs, and has severe consequences for animal health and trade.

Anyone keeping or working with cattle, sheep, goats or pigs should be aware of the symptoms, which include blisters on the mouth and drooling or limping animals.

The Department of Agriculture said a vaccine was available.