Agriculture Minister Murray Watt said the discovery was made during routine retail exercises, and the products - which were imported from China - have since been seized from several supermarkets and a Melbourne warehouse.

In a separate detection, a passenger who recently returned from Indonesia was found with an undeclared beef product that tested positive for foot and mouth viral fragments.

Mr Watt said although the discoveries were alarming, the detections showed the biosecurity system was working.

"Despite this, Australia does remain free from foot and mouth disease, and free from African swine fever," Mr Murray said.

"The fact that these pork products came from China rather than Indonesia show that this is not only an issue about what's happening in Indonesia."

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It's not the first time viral fragments of both diseases have been found at the nation's borders, however it is believed to be the first time fragments have been discovered in a retail setting.

Mr Watt said although much of the biosecurity focus had been on passengers returning from Indonesia, the advice from experts that the most likely way the viruses would enter the country was through contaminated products.

"Let's say for argument's sake [the virus] is in a piece of salami that gets imported to Australia, people eat most of the salami and throw the rest of it in the pig scraps - if pigs were to eat that, that could transmit the virus in Australia," Mr Watt said.

Mr Watt said investigations into how the products came into the country were underway and if any offences were found, prosecutions were likely.

"If you try to bring products into the country without declaring them, you will be caught," he said.

Biosecurity measures continue to be ramped up in response to the threat. The latest move is to roll out sanitised foot mats will be rolled out to all Australian international airports to service flights returning from Indonesia.

The foot mats follow several biosecurity announcements, including $9m for more biosecurity officers in airports and mailing centres, $5m to support the biosecurity systems of Indonesia, Timor-Leste and Papua New Guinea and one million FMD vaccines for Indonesia.

Mr Watt will meet with all state and territory Agriculture Ministers on Wednesday afternoon, where he is expected to give them an FMD update and discuss the National Biosecurity Strategy.