Dr Chris Parker, from the Department of Agriculture, Fisheries and Forestry, told the inquiry on November 15 that authorities still remained on high alert as they worked to prevent the disease from entering Australia.
"Our endgame is to assist them to get it under control," he told the inquiry.
"If it's under control, they're no different from the 70 countries around the world that have FMD (foot and mouth disease), and that then reduces the risk of incursion into Australia from a close neighbour."
Dr Parker said the latest figures showed about 575,000 animals had been infected with foot and mouth in Indonesia, which was up by about 1000 in the past few days.
He said Bali was on track to vaccinate all of its susceptible animals by the end of the year.
Dr Parker said Australia had provided about four million doses of the foot and mouth vaccine to Indonesia since August, with about 5,000,750 animals vaccinated since then.
He described the vaccinations as happening "at a pace" throughout the country.
Australia has also provided Indonesia with 435,000 doses to vaccinate against lumpy skin disease, which the country is also trying to contain.
Earlier the inquiry heard the foot and mouth outbreak in Indonesia had "kicked into gear" Australia's biosecurity system.
Red Meat Advisory Council chief executive Alastair James said the detection of the highly contagious livestock disease in a neighbouring country had focused the attention of industry and government.
"We've had the benefit of a crisis response without the crisis being here in Australia," Mr James said.
"So long as we keep the foot on the pedal we should be okay."
The inquiry was also told some media reporting had led international customers to incorrectly believe the virus had arrived in Australia.
Australasian Meat Industry Employees Union federal secretary Matthew Journeaux said unhelpful media reporting had sent "shockwaves" through his membership, with some falsely thinking foot and mouth had arrived in Australia.
The hearing was also told an industry task force formed this year had been meeting on a weekly basis for some time.
"We went back to fortnightly and now we're back to monthly because we are travelling along fairly well," Red Meat Advisory Council independent chair John McKillop said.
"There's a lot of work being done behind the scenes."
CSIRO also gave evidence on Tuesday.
The organisation's Dwane O’Brien said a national exercise would be carried out next year to see how Australia was placed to deal with an outbreak.
Dr O'Brien said part of the exercise would examine how long it took to get swabs from cattle into capital city laboratories for testing.
He said the CSIRO would be able to test samples and return results within 12 hours if the disease entered Australia, but there was a "huge variation" in the time taken to transport the swabs to the laboratories, depending on where cattle were tested.
