The research, reported in the British Medical Journal, concluded that schools may have to accept that sex education alone is not enough to combat other social factors affecting decisions about sex.
The evaluation was carried out in 25 non-Catholic east of Scotland secondaries and involved 8,430 pupils aged 13-15, one of the largest studies of sex education delivered by teachers. Some were on a new programme known as SHARE (Sexual Health and Relationships: Safe, Happy and Responsible).
The report said that the programme had no impact on behaviour, although pupils liked it and said it had improved their knowledge of sexual health. It had no effect, for example, on the use of condoms by the third of pupils who had sex by the age of 16.
Quality of teaching was not a factor in the limited impact on sexual behaviour. The main factors influencing sexual experience are the family, spending money and parental monitoring.
Daniel Wight of the Medical Research Council's social and public health sciences unit at Glasgow University, who led the study, said the aim now should be to see how the programme can be improved.
But Mr Wight added: "We need to develop and assess other methods of helping young people to make responsible individual choices, if affecting behaviour rather than just their knowledge and attitudes remains a core objective of school-based sex education."
The initiative involves an array of approaches to engage pupils in learning about sexual health, including interactive video and role-playing to improve "skills development".
The programme, which does not set out to encourage or discourage early sexual activity, is to be extended to more schools later this year, the Health Education Board for Scotland says. Its aims are to make sexual behaviour safer, cut unwanted pregnancies and improve the quality of relationships.
Its expansion was seized upon by Brian Monteith, the Tories' education spokesman, who has written to Cathy Jamieson, Education Minister, urging her to tell the Health Education Board to suspend sex education programmes. Mr Monteith wants them to be independently reviewed, with a greater input from parents.
A spokesperson for the Scottish Executive said the research had shown the need for a broad-ranging approach to issues like teenage pregnancies. "That is exactly the approach we are taking," he said. "There is no one single solution to the problem of teenage pregnancies in this country, which are slowly decreasing but still too high."