More than 20 per cent of babies born to mothers taking some anti-epileptic medicines during pregnancy are born with congenital malformations - but not taking them could put expectant mothers at risk.

A new awareness campaign launched today aims to highlight the importance of women using anti-convulsants talking to their doctors about the best way to keep themselves and their baby safe.

The medications could cause deformities or learning problems in babies but not taking them could pose a significant risk to expectant mothers.

"We need to drive home the critical message that women who take anti-convulsant medication need to discuss the risks and benefits with their doctor, even if they aren't actively planning on getting pregnant," said ACC chief clinical adviser Dr Peter Robinson.

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"There is a very delicate balance that needs to be struck.

"The harm caused by these medicines happens in the very early stages of pregnancy, often before you are aware you are pregnant, so it is important women know the potential risks and can plan accordingly. But it is equally important that women do not reduce, or stop taking, their medicine without speaking to their medical practitioner first, even if they think they are pregnant.

"The foetal risks can only be reduced by decreasing the dose or changing the medicine, but this must be balanced against the risk to the mother, especially if they have epilepsy as seizures can be life-threatening when not controlled by medication."

Robinson said that while all anti-epileptic medicine carried risk, sodium valproate carried the greatest risk with a reported rate of congenital malformations of up to 24 per cent for babies exposed to doses greater than 1500mg per day, compared with two to three per cent in the general population.

Children born to mothers taking doses of sodium valproate greater than 800mg a day in pregnancy had an average decrease in IQ of seven to ten points, and were eight times more likely to require educational intervention when they were six-years-old, he said.

Pharmac dispensing data indicated that 28,536 women of childbearing age took anti-epileptic medication in 2016.

The awareness campaign launched today was being run by ACC, the Ministry of Health, the Health Quality and Safety Commission, and Foetal Anti-Convulsant Syndrome New Zealand.

More information can be found here.

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