Senior doctors have called for male circumcision to be offered by the NHS amid fears that unregulated operations are leading to serious injuries among Muslim boys.

A number of public health specialists have urged the health service to overturn its ban on such operations after an investigation into circumcisions performed at an Islamic school in Oxford found that 13 out of 32 boys who had the procedure – at an average age of six – ended up with medical problems.

Three endured what a new research paper describes as "incomplete circumcision" at the hands of an overseas-qualified doctor who only had six months of basic surgical training. They also ended up with urethral scarring or a haematoma – a build up of blood that results from internal bleeding – or both. Six had to be treated in hospital for complications related to their circumcision, and two had to undergo the procedure for a second time. Ten of the 13 needed to take a course of antibiotics.

Writing in the UK Faculty of Public Health's Journal of Public Health, the study's co-authors, Dr Karthikeyan Paranthaman and two fellow public health doctors in Oxford, concluded: "This incident highlights the harm associated with circumcision in young children by unregulated operators due to lack of compliance with best surgical and infection control guidance. There is an urgent need for commissioning circumcision services for religious reasons in the NHS."

In 2006 the three specialists undertook an inquiry for the Thames Valley Health Protection Unit into unregulated circumcisions after an Oxford GP alerted them to a young patient. The procedures were carried out in the library of a faith school, they discovered. They listed a series of concerns about the way the operations were carried out.

They wrote: "All the children in this incident underwent the procedure under local anaesthesia, which is considered suitable only for newborns and infants. The use of physical force to hold the distressed child down [by one of their parents and an 'assistant nurse'] during the procedure, the absence of resuscitation training and equipment, [and] lack of follow-up care indicated the unacceptable standards of care.

"The appropriateness of the facility for conducting surgical procedures, inadequate decontamination of equipment and unsafe disposal of clinical waste were other significant issues of concern," they wrote. The General Medical Council banned the doctor involved from performing more circumcisions after it learned of the harm done to the boys.

The Oxford case was not an isolated incident, however. Tower Hamlets Primary Care Trust in east London began offering the operation to families who sought it for religious and cultural reasons in 2005 after some children were harmed in non-NHS procedures. "It was set up due to community need, and also to counter occasional children presenting at local accident and emergency departments with infections and other problems associated with unregulated operations," said trust spokesman Tim Carter.

The boys of parents who are registered with a GP in the borough can have the operation when they are aged between six weeks and five months. Parents are charged £120-£150. More than 900 boys have been circumcised by the Trust since the service began five years ago.

Most Jewish boys are also circumcised, without anaesthetic, usually when they are eight days old. Procedures are conducted by a "mohel" who, according to the Board of Deputies of British Jews, "is required to be a committed Jew and is very often a qualified doctor as well".

The mohel's duties "demand the highest standards of ethics, religious practice and surgical skills, including strict hygiene", the board says. It describes circumcision, or brit milah in Hebrew, as "the primary symbol of Jewishness for men". It reports no problems arising from the operations.

The Department of Health said it was not going to change its policy, despite the evidence of some boys suffering medical damage as a result of unregulated circumcisions. "On the NHS, circumcision should be carried out only for medical reasons," a spokeswoman said. "However, PCTs are responsible for commissioning services to meet the health needs of local communities. In some areas, particularly where they feel children are at risk from unsafe procedures, PCTs do work with local providers and communities to ensure that a safe and affordable service is available."