The NHS is accused today of failure, wasting money and missing key targets in its £150m campaign to curb the spread of the country's most common sexually transmitted disease.

Problems in implementing the £150m national chlamydia screening programme (NCSP) means the total number of under-25s tested for the infection is signficantly below target, says a National Audit Office (NAO) report. Only half of England's 152 primary care trusts manage to screen 26% of the young men and women in their areas for the disease, which if left untreated can lead to infertility, pelvic inflammatory disease and ectopic pregnancy. That is the minimum level of testing needed to ensure that the infection is controlled.

The NHS began testing under-25s for signs of the disease in 2003. But by 2007-08, just 4.9% of 15- to 24-year-olds were being screened. Even after the Department of Health made testing a priority in 2007, health trusts still missed the then 17% target.

Tests and follow-up treatment last year cost an average of £56 per person, although the Health Protection Agency, which oversees the NCSP, says that should be £33. Some £17m was spent unnecessarily last year because many primary care trusts paid too much for the tests, the audit office found. A total of 38,185 under-25s were tested last year, at schools, colleges and family planning clinics.

The NAO's highly critical report says:

• There was widespread "duplication of effort and cost" by trusts in implementing the programme, with the marketing and advertising of chlamydia testing services done with at least 45 different brands.

• 6,480 people who tested positive last year did not receive treatment, although 88% of people who did were given antibiotics.

• Almost three-quarters of trusts failed to trace and treat enough of the sexual partners of people who had tested positive.

"The delivery of the programme to date has not demonstrated value for money," the report says. "Annual testing of between 26% and 43% of young people is needed to significantly reduce the prevalence of chlamydia; only half of PCTs reached 26% or more in 2008-09, six years after the programme's launch."

Edward Leigh, chairman of the Commons public accounts committee, said: "This is a classic example of what can go wrong when a national programme is rolled out unthinkingly in a locally managed NHS. The department [of Health] should learn from this programme and not fall into the same traps again."

But Paul Ward of the Terrence Higgins Trust said the report was too negative. "It's clear that without the NCSP there would be tens of thousands of young people with chlamydia who would be undiagnosed, and many of them would be risking not only infertility but also transmission to others."

An independent assessment of the NCSP, commissioned by the health department and undertaken by public health specialist Dr Ruth Hussey, will today conclude that the increased rates of screening are a big improvement. "An ambitious new programme on this scale takes time to perfect and must continue to improve," said Gillian Merron, the public health minister.

Anne Milton, the shadow health minister who is an ex-nurse, accused the government of "throwing money at a problem without any real thought [and] abject failure in reaching their own targets on chlamydia", adding: "It is crazy that in some cases chlamydia is not being treated after detection.".