Coles supermarket says it does not solely rely on animal welfare rankings provided by an overseas organisation which farm groups have outed as animal activists.
In a statement, a Coles spokeswoman said it uses "a range of measures" to apply farm animal standards across its business and not just the little known UK-based Business Benchmark on Animal Welfare.
Farm groups this week said the organisation behind the assessment standard was looking to include a commitment for member businesses to reducing a reliance on animal products.
Woolworths has already indicated it is reviewing its involvement with this assessment group which has now been shown to be directly linked to the Austrian-based animal rights group Four Paws International.
It also has ties with UK-based "Compassion in World Farming", another animal rights group which says its mission is to end factory farming, citing beef feedlotting as an example.
The National Farmers' Federation and Queensland's AgForce, without naming the supermarkets directly, asked businesses assessed by the BBFAW to "rethink their links to the scheme".
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A consultation paper released by the organisation proposes to rank companies based on their commitment to "reducing reliance on animal products" - including a plan to halve the multi-billion dollar livestock industry by 2040.
NFF chief executive Tony Mahar said businesses should instead work directly with customers and suppliers to progress welfare outcomes.
"This proposal lays bare the agenda of the radical activist groups behind this benchmark.
"It's not about science-based improvements to animal welfare. It's an extreme agenda that puts livestock producers and their communities in the crosshairs," Mr Mahar said.
BBFAW lists Australia's biggest supermarkets Coles and Woolworths as having endorsed the benchmark.
The Coles spokeswoman said: "Coles has never set a tier target for the Business Benchmark for Farm Animal Welfare but our focus on high animal welfare has been recognised in BBFAW's ranking under the previous assessment criteria."
The spokeswoman said Coles would continue to use a range of measures of performance in animal welfare rather than the singular use of the business benchmark.
"We are committed to partnering with suppliers who have animal welfare standards that meet the high expectations of Coles and our customers," she said.
"We will continue to work with farmers, suppliers and industry partners to reduce environmental impacts through initiatives such as our Coles Finest Carbon Neutral beef range."
The BBFAW is believed to use publicly available system to makes its assessment of companies who may not elect to take part.
Four Paws and Compassion in World Farming provide "technical expertise and guidance on farm animal welfare and related issues, funding and practice resources".
The BBFAW says it is the leading global measure of farm animal welfare management, policy commitment, performance and disclosure in food companies.