The findings could have a major effect on future EU member government legislation concerning the addition of synthetic folates, a B vitamin, to flour.
The move was previously praised because the folic acid has been linked to the prevention of neural tube defects, such as Spina Bifida, in unborn babies.
While the IFR agrees that neural tube defects are reduced by adding folic acid to flour, the research body claims the move may also lead to a range of health problems.
Unlike natural folates, such as those found in leafy green vegetables, which are digested in the gut, synthetic supplements are metabolised in the liver, IFR scientist Sian Astley explained.
"The liver becomes saturated and un-metabolised folic acid floats around the blood stream," she said.
Once in the blood stream, the folates could provoke a number of complaints such as leukaemia, arthritis, bowel cancer and ectopic pregnancies in people already suffering from health problems.
"For women undergoing in-vitro fertilisation, it can also increase the likelihood of conceiving multiple embryos, with all the associated risks for the mother and babies," she added .
"It could take 20 years for any potential harmful effects of un-metabolised folic acid to become apparent."
Researchers called for further investigation into folic acid to gain a true picture of both the benefits and the risks of adding the supplement to flour across the UK.
New research is needed because scientists have assumed that folic acid is metabolised in the small intestine since the 1980s, the IFR said.
"We challenge the underlying scientific premise behind this consensus", Astley said.
"This has important implications for the use of folic acid in fortification, because even at low doses it could lead to over consumption of folic acid with its inherent risks".
In a statement, the FSA said that it had carefully considered any health risks associated with the move, including potential cancer risks.
The FSA originally agreed to recommend mandatory folic acid addition to either bread or flour at an open board meeting in May, saying that the decision has been made after "an extensive and scientifically robust assessment".
Deidre Hutton, the board's chair, said: "The FSA is committed to policy-making that benefits people's health… The board recognises that this move, as part of a package of measures, will help prevent birth defects in pregnancy and have wider health benefits for the rest of the population.
The board was also reassured by the significant science that the benefits outweigh potential risks."
Countries that have made the fortification of flour with folic acid mandatory include the US, Canada and Chile, while the move is currently being debated by regulators in Australia, New Zealand and Ireland. Source: British Journal of Nutrition "Folic acid metabolism in human subjects revisited: potential implications for proposed mandatory folic acid fortification in the UK ."
Authors: J Wright, J Dainty, P Finglas