UK biscuit and cake exports could be hit by the FSA's recommendation that folic acid be routinely added to flour.
The FSA told the Department of Health on Thursday that it believed fortification of bread with folic acid was desirable as part of moves to prevent spina bifida in unborn children.
It said the ingredient should be added at the milling stage as this would have less of an impact on the industry than if bakers were forced to do it when making bread. In papers released ahead of the meeting, the FSA said: "In terms of administrative burdens, the fewer the number of smaller firms impacted, the lower the cost to industry.
"Therefore the option of fortifying bread has a much greater cost compared to the other options as there are significantly more bakeries than mills in the UK."
The FSA estimated that fortification would cost each mill £20,000 per site.
But the Biscuit, Cake, Chocolate and Confectionary Association said the FSA's decision meant all flour, be it for bread or cakes, would contain folic acid.
This could affect the UK's £80m-a-year biscuit and cake exports because not all countries would be willing to buy in fortified products.
It could also hit farmers and millers in the UK because manufacturers might switch to unfortified flour from abroad.
"We know the FSA is conscious of this issue and are looking at the implications, and hope a compromise between health and business needs can be found," said Penny Hawley, director general of the BCCCA.