Australia's peak body for the vegetable industry believes community gardens pose a biosecurity risk for the country's horticulture sector.

The criticism comes on the back of the Federal Government scrapping the $1.5 million Community Food Grants program, created by the former Labor government under the National Food Plan.

Ausveg's William Churchill says his industry has welcomed that decision, and says the money could have been better spent developing export markets for growers.

"A lot of these gardens may not be in the best nick, so to speak, and the issue we then have is with infestations with either pests or diseases, and then that becomes a threat in itself to commercial horticultural operations that need to comply with strict adherence to quality assurance guidelines," he said.

"What happens when we start to get biosecurity risks is that growers may have to take pre-emptive action to prevent pests from arriving on their properties, and what that does is that it means they have to keep the product in the ground longer, rather than being able to get it out to consumers.

"So the end issue with having community gardens more prevalent out there is that a biosecurity risk becomes far more likely if community gardens start to grow."

Mr Churchill has also raised concerns about food safety at farmers' markets.

"We've seen a litany of examples where people have passed themselves off as other growers," he said.

"We have concerns there as well there about food standards and quality assurance programs that are in place."

But Michael Croft, from the lobby group Australian Food Sovereignty Alliance, says Ausveg has 'lost the vegetable plot', and that the real risks to Australia's biosecurity are not community gardens.

"By claiming the axing of community food grants was good policy, Ausveg is working against the best interests of Australian vegetable growers - particularly those that supply the domestic market," he said.

"To make matters worse, Ausveg repeats calls for further trade liberalisation - a double-edged sword.

"Free trade agreements, and the import competition they bring, are the main reason for Australian vegetable producers' woes, as the SPC Ardmona saga demonstrates.

"That Ausveg can't or won't see this fact beggars belief."

Mr Croft says community and fair food projects are not risky, and that, according to the Australian Bureau of Agricultural and Resource Economics and Sciences, they are the fastest growing sector in Australia.

"In attacking community and fair food initiatives, Ausveg are needlessly turning their fire on thousands of individuals and an increasing number of groups whose numbers include the strongest, best informed and most articulate supporters of Australia's horticulturalists," he said.

"These are groups and individuals that Ausveg should be applauding and supporting."