Coles started selling ‘sow stall free’ shopping bags in-store to help raise funds and awareness for the group on Monday in 500 stores across the country.
Animals Australia requested Coles withdraw the 'Make it Possible' bags in response to what they described as a "vicious campaign" against Coles and Wesfarmers.
The National Farmers' Federation (NFF) wrote to Coles chief executive Ian McLeod earlier this week urging Coles to seriously reconsider its position of support for Animals Australia.
NFF CEO Matt Linnegar said the animal rights group’s agenda was causing "serious harm to many parts of animal agriculture in this country".
Mr Linnegar said for Coles to partner with an organisation with a stated aim of eliminating meat products from supermarket shelves, “smacks of hypocrisy”.
"All we are doing is standing up for the rights of farmers - and I won't apologise for that," he said.
“Let’s be very clear: Australian farmers are committed to animal welfare. Our farmers raise, care for and nurture their stock and care deeply about what happens to them.
"We understand that improvements need to be made, but farmers, working with respected animal welfare groups, the community and governments, will be the ones who make them.
“Improving animal welfare is about changing behaviours. This will not be achieved by a group that simply stands on the sidelines and throws stones, which Animals Australia has proven itself to be."
A statement issued by Coles’ general manager, corporate affairs, Robert Hadler said Coles was concerned that their "good work with our farmer suppliers in the pork and chicken industries" would be overshadowed by farmer reaction to the Animals Australia campaign on live cattle exports, and agreed with the offer to withdraw the shopping bags.