Controversial scientific advice telling pregnant women to avoid using toiletries, processed food and non-stick frying pans is wrong and risks encouraging mothers-to-be to ignore vital health guidance, the nation's top doctor has told the Guardian.

Dame Sally Davies, the government's chief medical officer, said the recommendations in the study had taken the precautionary principle of minimising risk in everyday life to an absurd point and contained unrealistic and unnecessary suggestions, such as avoiding shower gel while pregnant.

Davies voiced concern that a paper produced by the Royal College of Obstetricians and Gynaecologists (RCOG) to warn pregnant women about the hazards of chemicals would increase their anxiety and confusion about how to safeguard their unborn child. Some would feel "overloaded or overwhelmed" with contradictory advice, she said.

"It fails the commonsense test by quite a long way. I think women will … lose faith in the important public health messages. If it does, as I fear it may take focus away from the chemicals that we do know cause real harm, in tobacco and alcohol – this isn't helpful," Davies said.

She was speaking after publication of the study on Wednesday led to claims that it was scaremongering and saw a host of scientific and medical experts dismiss its findings.

The study caused a row by suggesting that expectant mothers could reduce their exposure to chemicals by using fresh rather than processed food; shunning food and drink in cans or plastic containers, even in food storage; and minimising their use of toiletries and beauty products such as moisturisers, cosmetics, shower gels and perfumes.

The study was ridiculed for advising women, as part of a "safety first" approach, not to buy furniture, fabrics or non-stick frying pans while pregnant or looking after their other children.

Davies said media coverage of the recommendations risked causing mistrust of longstanding advice about drinking very little alcohol in pregnancy and not smoking. Between 6,000 and 7,000 babies are born each year with foetal alcohol spectrum disorder, and smoking while pregnant caused 2,200 premature births, 5,000 miscarriages and the death of 300 babies a year, she added.

"I think the precautionary principle and 'safety first' are being over-interpreted. I personally would not be avoiding shower gel and cosmetics. I have taken advice from Public Health England, who share my concern that we are moving away from a commonsense approach to a precautionary principle," said Davies.

Public Health England (PHE) told Davies that the paper's "messages are likely to cause concern and anxiety in relation to potential exposures to chemicals for which, as the authors acknowledge, there is no established evidence that pregnant women are at risk".

Dr John Harrison, director of PHE's centre for radiation, chemical and environmental hazards, backed some of the RCOG advice, including that pregnant women should avoid pesticides or fungicides. "However, there is no evidence to suggest that chemicals in items such as personal care products are a risk to public health," he said. Some of the RCOG's advice is based not on evidence of harm to humans but to animals, Davies added.

Tracey Brown, managing director of Sense About Science, a charity that promotes understanding of science, said Davies was right to criticise the paper. "They [the RCOG] have been irresponsible in putting it out to the general public rather than just to clinicians because they haven't thought about what the impact will be on pregnant women and, as Sally Davies said, not thought about how it will affect really sound public health advice, for example about taking folic acid [in pregnancy]."As a result of the paper, Brown added, "women are already raising concerns about things like whether they should buy new furniture for their nursery or paint their nursery. The risk is that people will start avoiding going swimming, because of chlorine in the water, or that people whose only vegetable with their meal is frozen peas will now not have frozen peas because they come pre-packaged."

The paper's suggestion that mothers-to-be may want to adopt a 'safety first' approach is also unhelpful because "means that people who can't avoid all these things are taking terrible risks and being very cavalier", she said.

The RCOG had no spokesperson available to respond to Davies's criticisms. It had hoped the study would increase awareness among mothers-to-be about chemicals that have been linked to "adverse health effects in women and children, including pre-term birth, low birthweight, congential defects, pregnancy loss, impaired immune development, as well as impairment of fertility and reproduction in both the mother and child in later life".