Official figures released to the Sunday Herald under Freedom of Information legislation show more than 400 children a year being diagnosed with chlamydia, gonorrhoea and syphilis.
Around one-quarter were in the NHS Lothian area, which covers Edinburgh, West Lothian, East Lothian and Midlothian - around 50% higher than might have been expected, given the health board's share of the Scottish population.
Most of those diagnosed were aged 15, around one-quarter were 14, but some were 13 and 12.
NHS Lothian and NHS Lanarkshire reported cases of chlamydia in 12-year-olds in 2010, 2011 and 2012, the last three years for which figures are available. NHS Greater Glasgow and Clyde has reported cases of syphilis and gonorrhoea in 13-year-olds since 2010.
The Scottish Government last night said it was down to councils to provide sex education.
Conservative health spokesman Jackson Carlaw said that sounded "like a rather casual dismissal of a serious and increasing problem", especially as SNP ministers had made a fuss of launching a sexual health website for young people.
Calling for a co-ordinated approach, he said: "This is a public health issue and it should be the Public Health Minister's priority to provide leadership. Parents … would expect nothing less."
The data, from Government agency Health Protection Scotland, represents the first published breakdown of STIs by age. Until now, published figures only referred to the under-19 or under-25 group.
The commonest STI diagnosed in under-16s was chlamydia. If left untreated, in women it can cause persistent pelvic pain, increase miscarriages and ectopic pregnancies, and lead to infertility. It can also cause infertility in men.
In 2010, there were 416 chlamydia diagnoses in 12 to 15-year-olds in Scotland, with cases in every health board except NHS Shetland. Of these, 330 were aged 15, and 72 were 14. The precise number of 12 and 13-year-olds was withheld in case it led to their identification. In 2011, there were 454 chlamyida cases, of whom 347 were aged 15 and 96 were 14. In 2012, the total was 400, of whom 302 were 15 and 93 were 14.
Covering 1.2 million people, NHS Greater Glasgow and Clyde had the highest number of diagnoses, with 112, 121 and 67 cases in 2010, 2011 and 2012 respectively, an average of 100 per year.
However, although it covers only two-thirds of the population of NHS Greater Glasgow, NHS Lothian averaged 104 cases a year - 83, 115 and 114 cases in 2010, 2011 and 2012.
The health boards for Lanarkshire, Grampian, Tayside and Ayrshire & Arran all averaged more than 30 cases a year in under-16s.
In the same three years, 49 cases of gonorrhoea were diagnosed in under-16s in seven health board areas, 23 of them in NHS Lothian.
Like chlamydia, it can cause infertility in women and men, and can also cause arthritis. A small but unspecified number of cases of infectious syphilis were found in 13 to 15-year-olds in NHS Greater Glasgow and NHS Lanarkshire.
Dona Milne, deputy director of public health and health policy at NHS Lothian, said: "We are encouraged that our education of the under-20 age group is proving effective and that more young people appear to be taking responsibility for their own health by taking up opportunities for STI testing."