Australia remains free of the diseases as the live virus was not detected, but Federal Agriculture Minister Murray Watt reiterated the importance of biosecurity measures.
The products, believed to be imported from China, were detected in the Melbourne CBD as part of routine surveillance and have been seized.
Senator Watt said it was the first time viral fragments had been detected in a retail setting.
"This is not the first time in Australian history that we have picked up foot and mouth disease viral fragments in meat products — it's happened a number of other times in airport settings," he said.
"I want to assure people that our systems have worked, we have monitored this, we have undertaken surveillance operations and these products have been found, tested and now seized."
Further investigations about how the products entered Australia was being taken and it was likely prosecutions would occur, Senator Watt said.
"If you do the wrong thing, you will be caught. If you try to bring products into the country without declaring them you will be caught," he said.
"If you try to bring or post products into the country, you will be caught and we will take action."
Sanitation mats will be rolled out at international airports in an effort to stop foot and mouth disease entering Australia on travellers’ shoes.
It's the latest measure by the Federal Government to prevent an outbreak of the livestock disease on Australian shores.
Travellers arriving in Australia from Indonesia will be asked to walk across the mats to sanitise their shoes.
The mats contain a citric acid solution, designed to dislodge any dirt from the sole of the shoe and cover it in the acid.
Other biosecurity measures include passenger declarations, profiling of all travellers entering from Indonesia, real time risk assessments, questioning and shoe cleaning.
Indonesia has been grappling with the spread of the disease which was recently detected in Bali, a popular holiday destination for Australian travellers.
If allowed to spread to Australia, the disease is predicted to cause an $80 billion hit to the economy over 10 years.
Senator Watt is set to meet with his state and territory counterparts for the first joint meeting in eight months to discuss further measures.
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