It seems like the most natural thing in the world to bring your baby into bed with you and give this tiny scrap of humanity all the closeness, comfort and reassurance you can. Mothers who do it know it quietens a fretful baby, and allows them to breastfeed without having to stumble out of bed into the shocking chill of the early hours in a half-dazed, sleep-deprived state of resentment.

But we must not do it, say authoritative bodies including the Department of Health and a leading charity. We must go against our instincts because we are risking our baby's lives. Bedsharing is a risk for cot death.

The Foundation for the Study of Infant Deaths (FSID) and the department say categorically that the safest place for a baby is in a cot in the parents' bedroom. Babies must sleep alone. Breastfeeding mothers should wake up, get up in the cold grey dawn, pick them up, settle in a comfortable armchair, feed them and then put them back in the cot and hope they won't wail piteously for long.

This message was strongly repeated by the foundation on the publication of a study this week by the British Medical Journal which FSID itself funded. "Latest findings by researchers from Bristol University . . . confirm that 'the safest place for a baby to sleep is in its own cot'. This four-year study . . . found that in half of all unexpected deaths of children in the south-west of England, babies had died sleeping with a parent or carer," said FSID's press release.

What is worrying, the release went on, is that 25% of mothers in a survey "were not persuaded that bedsharing can increase the risk of cot death".

But anyone who read the full paper, by a very experienced and well-respected team from Bristol and Warwick Universities, would be hard pushed to believe it either.

Yes – the study found that 54% of cot deaths occurred while the baby was co-sleeping with a parent. But although the risk was strong if they had crashed out on the sofa, it was only significant among those in a bed if the parent had drunk more than two units of alcohol or had been taking drugs.

This is a serious, heavyweight piece of research by a team with impeccable credentials who have been working in this field for 20 years. They looked at all sudden unexplained infant deaths (Sids – often referred to as cot deaths) in the south-west of England between the start of 2003 and the end of 2006. After campaigns in the 90s on the dangers of putting babies to sleep on their fronts, the number of cot deaths has dropped dramatically – by half. But there were still enough deaths (79) in this study to make their conclusions valid.

Peter Fleming, professor of infant health and developmental physiology in Bristol, one of the study authors, was appalled by the misinterpretation, as he sees it, of the paper in the media this week. "I really felt quite uncomfortable about it," he told the Guardian yesterday.

"My view is that the positive message of this study is that it says don't drink or take drugs and don't smoke, particularly for breastfeeding mothers. We did not find any increased risk from bedsharing. It is a very different message from the one the media picked up."

You can say that half the deaths occurred while babies slept with their parents. You could also say that half the deaths occurred while babies were alone in their cots, he says, but: "I don't see anybody saying, 'Don't put your baby in a cot.'"

Fleming has a particular reason for worry. The study showed that sleeping with the baby on a sofa really is a risk. Yet seven of the parents whose baby died say they had gone to the sofa to feed, aware that bedsharing is said to be dangerous, and had fallen asleep.

"Any advice to discourage bedsharing may carry with it the danger of tired parents feeding their baby on a sofa, which carries a much greater risk than co-sleeping in the parents' bed," says the paper. "Anecdotally, two of the families of Sids infants who had co-slept on a sofa informed us that they had been advised against bringing the baby into bed but had not realised the risks from falling asleep on the sofa."

But despite Fleming's concern, the FSID was sticking to the line agreed with the Department of Health yesterday: "The safest place for an infant to sleep is in a cot beside the parents' bed." It pointed out that the same sentence appears in Fleming's paper, but did not mention what follows next: "Based on evidence from research into Sids it is questionable whether advice to avoid bedsharing is generalisable and whether such a simplistic approach would do no harm. Parents of young infants need to feed them during the night, sometimes several times, and if we demonise the parents' bed we may be in danger of the sofa being chosen. A better approach may be to warn parents of the specific circumstances that put infants at risk."

Joyce Epstein, director of FSID, says this is too complicated. "If you can get people's attention for more than three seconds you would like to give the whole story every time, but at what point do you lose everybody?" she says. From their perspective, the simple direct message – put your baby to sleep in a cot near the bed, not in the bed, is the key.

The new study, she says, is just one study (although in a Lancet 2006 paper the Bristol team also found a link to drink and drugs). George Haycock, professor emeritus of paediatrics at St George's hospital in London, who is FSID's scientific advisor, points to nine previous studies that have looked at co-sleeping and cot death and concluded that sharing a bed is risky.

"You can't say there is no risk," says Haycock, even if it is small for non-smokers. And he is tacitly critical of the "breastfeeding lobby" for defending bedsharing, when there is no concrete proof that it increases the numbers of women who breastfeed.

But Fleming says this study breaks new ground. Nobody in the past has gathered reliable information about drug-taking. "The advantage of this study is that because we did a death-scene evaluation, three to four hours after the baby died, we were able to look at all sorts of factors which in the past we couldn't look at." When the researchers talked to the parents, offering sympathy without blame and the possibility of explanations for their tragic loss, the parents told them everything, including what they had drunk and what drugs they took the night before. "People are very willing to share that information with you at that time," he says. "You get the real picture."

The paper adds that the findings may explain some of the quirky cultural associations between co-sleeping and Sids. Among black African populations in the United States and Maori and Aboriginal people, where babies commonly sleep with their parents, cot deaths are high, yet in other bedsharing communities, such as Japan, Hong Kong and among the Bangladeshi and other Asian peoples of the UK, deaths are low. The difference is in their smoking, drinking and drug habits.

FSID's raison d'etre is to eliminate sudden unexpected infant deaths and that is what they believe their advice on putting babies in cots, on their backs, "feet to foot", on a firm mattress with no pillow, will help do. But other organisations think there may be real benefits to taking your baby into your bed. The National Childbirth Trust (NCT), the country's leading parenting organisation (and champions of breastfeeding), openly defends bedsharing.

"The study shows that risks for babies whose parents did not smoke or consume alcohol or drugs but who did share their bed with their baby were not different from that for babies in a separate cot," says its head of research Mary Newburn in a statement responding to the BMJ publication.

The NCT's position is a response to the real world of its members. "Many parents share their bed with their baby when they are young and this can be done safely," says Newburn. "It is clear from surveys that around half of parents sleep with their babies at some point in the first six months, and around a quarter do so routinely, so we need to help them to do this in the safest way possible."

Rosie Dodds, NCT senior public policy officer, says they understand FSID's position. "They are really worried about the number of babies dying and want everybody to be as safe as possible," she says. "But there are likely to be advantages to babies sharing a bed with parents." Although she acknowledges that there is no scientific evidence establishing that bedsharing increases breastfeeding, there is an association, and breastfeeding on its own has been shown to lower the risk of cot death.

Deborah Jackson, author of Three In A Bed, says she thinks we are, in the UK, "fixated on the bad aspects of sharing a bed with the baby", which is strange because "the history of bedsharing or shared sleeping places with the baby is as old as humanity itself".

Her research, together with her own experiences of bedsharing with her three children, have persuaded her it is profoundly beneficial for both mother and child. The mother is aware of her baby as she is sleeping and reacts to her. "[Once] I was asleep," says Jackson. "[One of my children] was sleeping next to me. I suddenly sat up in the night and held her over the bed and she was sick," she says. Somehow she had known the baby was about to be unwell.

But there are clear dangers if the mother has been drinking or taking drugs. "All the things that make it good can make it really dangerous if you are not incredibly sensible. That's true of everything in parenting," she says.

Cot death is devastating and everybody is on the same side – they want to see fewer tragic families who have lost their babies. But there is clearly not one single road that everybody can march down together. In the end, a single prohibitive message for parents may even be counter-productive. This may be one of those cases where the public should be given credit for their intelligence and allowed to make up their minds on the basis of rather fuller information.