Their findings, based on research covering more than 13 million births, offer a strong argument for governments to move towards food fortification.
Trials showed more than a decade ago that folic acid can reduce the occurrence of neural tube defects, such as spina bifida, by half or more. This prompted some countries, including the US, Canada and Chile, to introduce mandatory fortification of flour with folic acid.
The initiatives have paid off. In Canada, which introduced folic acid fortification in 1998, the prevalence of neural-tube defects among both unborn and newborn children has been halved and it has also had a similar benefit on incidence of the deadly childhood cancer neuroblastoma.
However most other governments have tried to promote use of folic acid supplements rather than increasing intake of the vitamin for the whole population.
But there are problems with this type of intervention. The neural tube is fully developed 22 to 28 days after conception but many women are not aware they are pregnant until after this time. Starting folic acid supplements after this period is too late to protect against birth defects.
The new study, published in the British Medical Journal online edition, provides further evidence that recommendations to take supplements are not enough to prevent neural tube defects.
Using data from over 13 million births in Europe and Israel from 1988 to 1998, the researchers identified cases of neural tube defects, and policies and recommendations regarding folic acid. They found no "detectable impact" of such recommendations.
"We estimate that thousands of pregnancies that would otherwise have been healthy were affected by neural tube defects in the study area alone since 1992," write the authors.
"These findings, which support and expand those from an earlier study…, underscore the ongoing missed opportunities for prevention well after publication of the confirmatory randomized clinical trials and the first public health recommendations."
Each year about 3 per cent of all new births around the world are affected with major structural birth defects, according to the new study, or more than 4 million each year, and these are the major cause of infant mortality and disabilities among children in industrialized countries.
However Europe remains fearful of possible side-effects of a wide-ranging fortified food initiative. A two-year investigation into flour fortification by the UK's Food Standards Agency concluded in 2002 that this could mask a deficiency of vitamin B12 in elderly people.
The new findings are most likely a result of recommendations not being implemented widely enough to produce a sustained change in behaviour in a sufficiently large proportion of women to cause measurable effects, say the authors.
"In general, use of supplements tends to follow economic and educational lines, so targeting the entire population through recommendations on supplementation alone may not be practical," they note.
They add that flour fortification can cross these social and economic boundaries.
"A reasonable and urgent strategy to reduce this growing and unceasing burden of preventable death and disability is to quickly integrate fortification with a fuller implementation of recommendations on folic acid."