Abortions for cleft lip and palete are ten times more common than is being reported, according to a European register.
The Department of Health recorded 14 such abortions in England and Wales between 2006 and 2010, using data from the forms doctors have to fill in when carrying them out.
But Eurocat, which registers congenital abnormalities, said 157 abortions for cleft lip and palete have taken place in the same period.
The European register tracks what happens to a foetus once it has been identified with an abnormality.
Its information comes from foetal medicine specialists, ultrasonographers and genetic testing laboratories.
The Department of Health said: “We are aware that there is a potential discrepancy in figures and are looking into this in further detail.”
Eurocat also looked at abortions for club foot.
In 2010, it said 37 were aborted for this reason.
Stuart Campbell, an obstetrician and a specialist in diagnosing cleft lip and club foot by ultrasound, said: “Club foot is treatable. To have 37 babies aborted in one year is an awful lot. This is horrific.”
The Department for Health came under fire recently for its under-recording of Down’s Syndrome abortions.
According to the National Down Syndrome Cytogenetic Register, 942 babies with the condition were teminated in 2010.
But the Department of Health only recorded 482 abortions for the condition, showing that 49 per cent were not reported.
Dr Peter Saunders, chairman of the Christian Medical Fellowship, said the discrepancy could point to problems with abortion reporting on a larger scale.