The number is almost double previous estimates.
The report, from the British Isles Network of Congenital Anomaly Registers (Binocar), estimates there were at least 14,500 babies with birth defects in England and Wales in 2009.
However, Joan Morris, professor of medical statistics at Queen Mary, University of London and editor of the report, said researchers did not believe the overall incidence of birth defects is on the rise.
"We know that the incidence is not increasing," she said.
"What we are now saying is that we have good figures on what it actually is."
The report said the most common defect is congenital heart disease, which affects at least five in 1,000 babies and can require major surgery.
Around 6 per cent of babies born with a heart defect will die before the age of one. Neural tube defects, such as spina bifida, affect one in 1,000 babies.
Most of these cases could be prevented through women taking folic acid supplements while trying to conceive and during early pregnancy.
Gastroschisis - a defect where the intestines develop outside the abdomen - affects one in 1,000 babies.
Incidences of cleft lip and/or palate is 15.2 per 10,000 babies. London has the highest prevalence of Down's syndrome (34 per 10,000 babies) while the North West had the lowest (21 per 10,000).
The report said these differences "probably reflect the different maternal age distributions", with mothers in London tending to be older, thereby having a higher risk of Down's.
More than half of all birth defects studied in the report were detected during pregnancy. Where the birth defect was detected in pregnancy, 43 per cent resulted in a termination.