Fragmented implementation of the programme across PCTs has been 'nonsensical' and has failed to provide value for money, the watchdog said.
Standard funding and service specifications for GPs and other service providers should be developed so that cost-effective chlamydia screening services can be offered in all PCTs, it reported last week.
The NAO reviewed implementation of the programme since it began in 2003. It estimated that if all trusts had delivered tests cost-effectively, savings of £17 million a year could have been made.
But the cost of failing to deliver services cost-effectively is rising in line with uptake of testing and will hit £40 million this year unless changes are made, the NAO said.
Its estimates are based on research by the Health Protection Agency (HPA), which is developing model contract specifications for chlamydia screening in GP practices.
An HPA spokeswoman told GP its guidance would help PCTs set fair funding for providers. Currently, local enhanced service payments vary from £1 to £15 for testing and from £8 to £100 for treatment and partner notification, the NAO found.
Mark Davies, NAO director of value for money studies, said PCTs were also failing to make the most of potential economies of scale. 'It seems nonsensical for PCTs to buy testing kits and treatment on a PCT-by-PCT basis,' he said.
The NAO found that prices paid by PCTs for testing kits also varied, from 50p to £44 per kit. Some PCTs have also failed to achieve levels of testing necessary to reduce infection levels.