A quarter of patients are having to wait more than two weeks for a sexual health clinic appointment, research published today shows.

The Health Protection Agency (HPA) research also found that fewer than half of patients (45%) were offered appointments within two days; in more than two-thirds of cases (67%), this was because the clinic was too busy to be able to offer an earlier appointment.

The government set a target for every patient to get an appointment at a sexual health clinic within 48 hours by 2008 in last year's public health white paper.

Figures for 48-hour waits were adjusted this year to take account of weekends. Using the old methodology, which includes waiting over weekends, there was a slight increase in the proportion of people seen within two days - from 38% in May 2004 to 40% in May 2005 - but the HPA report did not consider this improvement "substantial".

The HPA, the body that monitors rates and outbreaks of infectious diseases, identified a north-south divide in the treatment of STIs with patients in the north waiting far longer for an appointment.

The longest waiting times were in the north-east, where fewer than a third of patients (29%) were seen within 48 hours and 43% had to wait more than two weeks for an appointment. This was followed by the West Midlands, where 31% were seen within two days and 42% had to wait more than a fortnight.

The shortest waiting times were in London, where 62% of patients were seen within two days and 13% had to wait more than two weeks. The second best results were in the south-east, where 49% of patients were seen within 48 hours and 27% waited longer than two weeks.

A Department of Health spokeswoman said the figures showed waiting times were "stable".

She added: "We recognise there is still a long way to go before we meet our 2008 target of giving everyone who needs it an appointment within 48 hours. And we have responded to this by committing an extra £130m for genitourinary medicine services between 2006 and 2008 - allowing clinics to expand their services and offer more and more people access to early treatment."

But the Family Planning Association (FPA) said the figures showed sexual health clinics were "overwhelmed" and called for GPs to offer treatment to meet the rising demand.

Toni Belfield, the FPA's director of information, said: "This report shows genitourinary medicine clinics are overwhelmed with demand and provides an opportunity to look at their workload by expanding treatment for sexually transmitted infections within general practice. "General practice can be ideally placed to take on treatment and prevention of STIs as it has a much wider reach than clinics can ever achieve."

The survey found that women had to wait longer than men for an appointment, with only 43% seen within two days compared with 47% of men. According to the FPA, this is because the tests and treatments for women are more complicated.

More than three-quarters (76%) of patients seeking emergency treatment were seen within 48 hours, compared with just over a quarter (26%) making routine appointments. Those attending walk-in clinics were seen most promptly with 81% seen within two days.

Long waiting times increase the spread of STIs, according to research by charity the Terence Higgins Trust. It has found that around 30% of people waiting to be seen at genitourinary medicine (GUM) clinics continue to have sex, despite showing symptoms.

The survey, carried out in May 2005, covered 199 (97%) of England's 205 GUM clinics.

The report called on primary care trusts and strategic health authorities to invest more money in GUM clinics. The government announced a further £15m for NHS sexual health services in July.

The latest HPA figures on the prevalence of STIs in England show infection rates rising. For example, 103,932 new cases of clamydia across England, Wales and Northern Ireland were diagnosed in 2004, an increase of 8% on 2003. And 79,618 new cases of genital warts were found in 2004 - an increase of 4% on the previous year.