Agriculture Minister Murray Watt says $14 million will be spent on combating the spread of the disease in Australia and overseas.
Of that, $5 million will go towards on-the-ground measures in Indonesia, Timor-Leste and Papua New Guinea, including technical assistance and epidemiological support.
A further $9 million will be spent on 18 new biosecurity officers to be stationed at Australian airports and mail centres, as well as detector dogs in Cairns and Darwin.
Funding will also go towards a new northern Australia co-ordinator to manage surveillance and preparedness strategies across the region.
Senator Watt warns the disease could cause an $80 billion hit to the economy if it's allowed to spread in Australia.
"We need the travelling public to take this seriously," he said.
"If foot and mouth disease gets into our country it will be a devastating blow for our agricultural industry, particularly our livestock industry.
"While there is a lot of attention on the travelling public coming back from Indonesia ... the highest-risk way of foot and mouth disease coming back into our country is through animal products, meat products and dairy products."
NSW Premier Dominic Perrottet said a balance needed to be struck between relaxed travel restrictions and protecting the farming industry.
"We need to make sure we act quickly and err on the side of caution because the devastating impact that (FMD) can have, particularly on our agricultural providers in rural and regional NSW, is significant," he said.
Nationals leader David Littleproud welcomed news of additional funding to prevent the disease's spread, but said the government was too slow with the uptake of the measures.
"They have taken too long to reach out to Indonesia, too long to bring forward biosecurity spending and still cannot make up their mind on foot baths and mats," he said.
"The minister says FMD is a small risk, yet the advice I was provided by the department said there was an increase to 18 per cent chance of transmission to Australia once FMD was in Bali."
The Nationals previously called for the government to introduce compulsory shoe decontamination and a two-day ban from returning to regional Australia following the outbreak.
The federal government had previously provided $1.5 million for at least a million doses for Indonesia's foot and mouth vaccine program, following a formal request for assistance after the disease spread to Bali.
Senator Watt said as a result of that spread the government was risk-profiling passengers returning from Indonesia.
"If any of those passengers match the risk profile ... then those passengers are screened and go through ... being questioned, having shoes cleaned, having luggage examined, having detector dogs," he said.
National Farmers Federation president Fiona Simson said Australia needed to pull out all the stops to prevent the spread of the disease.
"While we welcome today's announcement, we still want every single traveller returning from Indonesia screened and for constant review of all settings in out line of defence," she said.
"We urge every traveller to be vigilant by avoiding farms in Indonesia, thoroughly cleaning their clothes, or even better, support our Throw Your Thongs campaign."
For more information on FMD visit: www.agriculture.gov.au/footandmouthdisease
