Women who took the drug during pregnancy to treat epilepsy were four times more likely to give birth to babies with congenital malformations, said the report, jointly issued by the French National Agency for the Safety of Medicines (ANSM) and the national health insurance administration.
"The study confirms the highly teratogenic" -- that is, capable of causing birth defects --- "nature of valproate," Mahmoud Zureik, scientific director of ANSM and co-author of the report, told AFP ahead of its release.
"The figure of about 3,000 severe malformations is very high," he told AFP in an interview before the findings were made public.
The types of birth defects attributed to the drug included spina bifida -- a condition in which the spinal cord does not form properly, and can protrude through the skin -- as well as defects of the heart and genital organs.
The risk of autism and developmental problems was also found to be higher, and will be quantified in a follow-up report due later this year.
An earlier estimate suggested that 30 to 40 percent of children exposed in the womb could suffer such disorders.