The livestock disease, which affects pigs, cattle, sheep and goats, was detected in Indonesia in May and spread to Bali last week.
NSW Agriculture Minister Dugald Saunders says that with 103 flights each week from Australia to Bali "FMD is the closest it has ever been to our country".
As Australian travellers return to the holiday destination in droves, NSW Deputy Premier Paul Toole has warned of the threat to the cattle industry and the livelihoods of thousands of farmers across NSW.
"Nobody wants to be the person who brings in a disease that would devastate our livestock industry, cost the economy $80 billion, and shatter regional communities for years to come," he said on Wednesday.
"We want to make sure that 100 per cent of passengers returning are being screened.
"I don't care if it takes an extra two hours for a passenger getting off a plane", Mr Toole told reporters at Sydney Airport's International Terminal.
"It's better to be safe than sorry".
The government is advising that when entering the country travellers must ensure their clothes and shoes are clean and free from soil and manure, otherwise, it's best to leave them in Indonesia.
Australians should also stay away from livestock for a week after their return.
Around 1.3 million Australians visited Bali in 2019, before the COVID-19 pandemic.
Dairy NSW Regional Officer Alicia Richters warned the repercussions of the disease hitting the industry would be felt by every Australian consumer.
"You're not going to buy your morning coffee anywhere," she said.
"We've already been devastated this year with significant flooding, we had our fourth flood only last week.
"It would take a massive toll not only on our producers but the service industry too".
Mr Toole said discussions with the federal government and other states had taken place about implementing stringent controls for returning holiday-makers.
Federal Agriculture Minister Murray Watt is visiting Indonesia this week to gather more information about how it's containing the contagious disease.
Mr Saunders said a potential vaccine was being developed using mRNA technology to tackle eight different strains of the disease.
But NSW Farmers policy head Annabel Johnson stressed the onus was on travellers to do their part in keeping the disease at bay.
"This is a critical risk," she said.
"We're asking travellers... to make sure you're declaring, make sure your clothes and shoes are clean ... or leave them."
"Prevention is better than the cure ... We must keep this out".
