Agriculture Minister Murray Watt on Friday authorised the establishment of biosecurity response zones in the nation's international airports where travellers into Australia can be screened more thoroughly.
Travellers would be directed to comply with biosecurity measures, including removing their shoes or walking over sanitation mats, and be questioned by officers.
It's the first time the Biosecurity Act powers have been used in Australia.
"I had been concerned about some rare reports that some return travellers were not doing the right thing when returning from Indonesia," Senator Watt said.
"These zones strengthen and widen the powers of biosecurity officers to direct passengers to use foot mats and other biosecurity control measures such as the cleaning of shoes."
The outbreak in Indonesia spread to Bali, a popular destination for holidaying Australians, about two weeks ago.
Senator Watt has already announced a $14 million package to help reduce the risk of the livestock disease spreading from Bali to Australia.
The package will provide one million vaccines for the Indonesian cattle industry and boost measures in Australia to increase detection and protect the local industry.
"We have wasted no time in getting on top of this issue and have been consistently ramping up measures at our airports and mail centres around the country," the minister said on Friday.
But Nationals Senator Bridget McKenzie, who is the coalition spokeswoman for infrastructure, transport and regional development, said it was not enough.
"The government now has been flat-footed on this," she told Nine Network on Saturday.
"We have known that this outbreak occurred just across the waters in Indonesia from May.
"We are only just now seeing measures where they're starting to take it seriously with mandating shoe cleaning and the like."
Viral fragments of foot and mouth disease were detected in pork products at a Melbourne retailer this week.
But Australia remains free of the disease, as the live virus hasn't been detected.
Senator Watt has already rejected opposition calls to ban flights from Indonesia and has dismissed criticism the government hasn't acted fast enough.
Senator McKenzie wants the border closure option to remain on the government's table.
"We can't emphasise enough that the kitchen sink needs to be thrown at this," she said, adding the threat will dominate question time when federal parliament sits next week.
The Department of Agriculture has estimated the direct economic impact of a large multi-state foot and mouth outbreak over 10 years at around $80 billion.
The disease is highly contagious and affects cattle, sheep, goats, camelids, deer and pigs.
The virus is carried by live animals and can present in meat and dairy products, soil, bones, untreated hides, vehicles and equipment used with farm animals.
It can also be carried on clothing and footwear and survive in frozen, chilled and freeze-dried foods, according to the department.
