Britain's top children's doctor has said that more than 10,000 babies each year suffer serious harm, including death, because their mothers drank alcohol, smoked, over-ate, or took drugs during pregnancy.

Professor Terence Stephenson, president of the Royal College of Paediatrics and Child Health, said newborns are suffering permanent harm including brain damage, disability or physical deformity. Others die because of miscarriage or stillbirth caused by their mother's smoking.

What he called "avoidable [and] self-inflicted" harm to unborn children represented a major public health problem, an ongoing human tragedy and a high cost to the NHS, he said.

"There's going to be tens of thousands of babies being harmed from the effects of women smoking or drinking in pregnancy and if we're talking permanent damage it's going to be over 10,000", said Stephenson, who is also an expert at the Institute of Child Health in London.

He said that an estimated 6,000 of the UK's 800,000 babies a year are born with some form of fetal alcohol spectrum, which can cause brain damage, physical problems and learning disabilities. The fact that 18% of expectant mothers binge drink by consuming six units or more in a single session at least once while pregnant was very worrying, Stephenson said.

One third of women smoke in pregnancy, which increases the risk of miscarriage, complications in pregnancy such as bleeding or a detached placenta, birth defects and cot death. Babies born to mothers who smoke in pregnancy are also a third more likely to be stillborn or die within a week of birth, research shows. Some 17,000 babies a year receive hospital treatment because of passive smoking.

"These are difficult things to give up, and we still see worryingly large numbers of women in pregnancy exposing their children to harmful substances. Some are choosing to indulge in these behaviours – recreational drugs, alcohol and smoking – that are not essential things for life", he added.

"We're a developed country. We've got rid of polio and diphtheria – big childhood killers. [Yet] these are avoidable causes of child harm and death and we as paediatricians would like not to see them at all. You can choose not to smoke, not to drink.

"So it's not an act of God. It's harm that's being caused by the actions of parents. You choose to have a pregnancy. It's a normal biological process. The general outcome is health. Why would you want to risk that with something that's in your gift?"

Stephenson's comments follow a growing body of medical evidence blaming smoking and drinking in mothers-to-be for harming their babies' health.

Smoking in pregnancy was this summer linked by researchers led by scientists from University College London to birth defects in babies such as missing or deformed limbs, facial disorders, club foot and gastrointestinal conditions. An American study this year found that teenagers are much more likely to be unruly, aggressive and badly behaved if their mothers drank early in their pregnancy.

Young women need to do more to prepare themselves before conceiving as the harms identified by Stephenson are "a big issue", the British Medical Association said. "We need young women who are planning to become pregnant to get into the right physical state: stop taking drugs if they do that, stop smoking and either stop drinking or cut down to a very, very low level – one or two units a week," said Dr Vivienne Nathanson, its head of science and ethics.

Changes in behaviour would come about through helping young women, not preaching at them, she said. Smoking cessation services needed to be targeted at women from poorer backgrounds, who were more likely to use cigarettes,women's partners should be encouraged to quit smoking as well, to make it easier for the woman, and boys as well as girls told about the risks of smoking in pregnancy during school Personal Social Health and Economic education classes. "There are no simple answers" she added.

Health secretary Andrew Lansley endorsed Stephenson's concerns. "Every child deserves to have the best possible start in life and it is clear that drinking more than the recommended guidelines or smoking when pregnant can harm your baby," he said.

While NHS doctors, nurses and midwives were working hard to address these behaviours among pregnant women ministers were also pursuing other measures through the Responsibility Deal and the Tobacco Control Strategy's aim of cutting rates of smoking throughout pregnancy from their current rate of 13.2% to 11% or less by the end of 2015.

Mothers-to-be should ideally consume no alcohol whatsoever but, if they drink at all, should limit themselves to one or two units once or twice a week, Lansley added.

Case study

Margaret (not her real name), who is 40, has 15- and 10-year-old sons who both have fetal alcohol spectrum disorder.

"The day the geneticist diagnosed my sons was the worst day of my life because I realised that my behaviour had affected my children. I was devastated. My drinking had caused my children to have a lifelong disability. He said they had 'a neurodevelopmental disorder that is related to alcohol'.

Strangely my older son is more affected than my younger one, even though in my first pregnancy I was drinking less. With my second child I was drinking a lot more because I was an alcoholic by then, though I didn't realise that at the time. But then, fetal alcohol damage is not consistent; it affects different people in different ways.

Alcohol in pregnancy is like buckshot to the baby's brain. It can affect a baby's ability to remember stuff, store information or get the consequences of actions. While every child affected by it is different, they have some of the same traits: impulsiveness, distractability and disorganisation, for example. It can cause problems at nursery or primary school and lead to truancy and children being accused of lying, although the reality is that they simply can't remember what someone told them the day before.

You can tell some children who have severe FASD because their facial features are unusual. But the brain can be damaged even if the child looks normal. Neither of my two sons' faces are unusual, but both their brains are affected. They are beautiful children: loving, kind, very creative and athletic and outgoing. But they do have some problems as a result of this.

When the older one was young, people thought he was the problem because he was acting up at school and so on. But with my younger son it is regarded as the problem, especially since they were both diagnosed five years ago.

In pregnancy you are told not to smoke or take drugs and avoid certain foods, but midwives don't tell you that your drinking can cause FASD. They should stop being so reluctant to raise it. Women need to realise that it's like Russian roulette: if you drink a certain amount you could be putting your baby at risk. Husbands and boyfriends need to be educated about this too, not just the women."