It suggests that 15,000 women a year in England suffer an infection after their caesarean birth, the researchers said.
The study found that 9.6 per cent of women having caesarean section births developed an infection afterwards compared with just 6.6 per cent of women having a hysterectomy.
As one in four births are by caesarean, experts said the infections are a serious problem for both patients and add extra costs for the NHS.
Being overweight, aged under 20 and having the operation performed by a more junior doctor than a consultant increased the risk of infection even more.
The study investigated almost 400 infections in more than 4,000 caesarean births during 2009.
The findings were published in the British Journal of Obstetrics & Gynaecology surprised experts because the operation is considered relatively 'clean' unlikely surgery involving the large bowel which results in 13 per cent of patients suffering infections.
Of the 394 women who developed an infection, the majority had been given antibiotics as a precaution.
Most infections were not serious however seven per cent were more serious and would have required an additional stay in hospital and a further five per cent were deep infections which may have required further surgery.
Women who were overweight were 60 per cent more likely to develop an infection and those who were obese were almost 2.5 times more likely to have an infected wound.
Women aged under 20 were almost twice as likely to have an infection compared with those aged 25 to 30 and having an associate specialist or staff grade doctor perform the operation instead of a consultant increased the risk by 60 per cent.
Dr Elizabeth Sheridan, Head of Healthcare Associated Infections at the HPA, said: “Reducing rates of surgical site infections following a caesarean should be made a priority.
"Given that one in four women deliver their baby by caesarean section, these infections represent a substantial burden. They will impact not only directly on the mother and her family but also are a significant cost in terms of antibiotic use, GP time and midwife care and every effort should be made to avoid them.
"Women choosing to have caesarean section for non-medical reasons should be aware of the risk of infection, particularly if they are overweight.
“As has been seen in both this study and several others, there is an established link between BMI and an increase in the risk of developing a surgical site infection.
"Monitoring infections in women having a caesarean section is important as a means to drive down infection rates.
"As levels of obesity are rising, optimising surgical techniques and identifying the most appropriate dosing of antibiotics could provide a means for reducing wound infections in obese women.”
Lead author Dr Catherine Wloch, Department of Healthcare Associated Infection and Antimicrobial Resistance at the Health Protection Agency said: “This study has identified high rates of surgical infection following a caesarean with one in ten women developing an infection. Whilst our study didn’t measure this, these infections are likely to have an impact on a woman’s experience and quality of life.
“Although most caesarean section wound infections are not serious, they do represent a substantial burden to the health system, given the high number of women undergoing this type of surgery. Minor infections can still result in pain and discomfort for the woman and may spread to affect deeper tissues. The more serious infections will require extended hospital stays or readmission to hospital.
“Prevention of these infections should be a clinical and public health priority.”
John Thorp, BJOG Deputy-Editor-in-Chief said: “With the rise in numbers of women having a caesarean section and the rise in obesity rates, this issue is an important one.
"Post-surgical infection can seriously affect a woman’s quality of life at a critical time when she is recovering from an operation and has a new born baby to look after. More needs to be done to look into this and address ways of reducing infection.”
Gail Johnson, education and professional development advisor at the Royal College of Midwives, said: “This further supports the need to ensure that any caesarean section is performed only where clinically indicated, following full and detailed discussion with the woman, the midwife and the obstetrician in accordance with guidelines.
"Women who develop an infection postnatally are likely to feel less able to provide care to their baby and will take longer to recover from the birth.