The row has broken out as new figures from the Office for National Statistics revealed more 13- to 15-year-old girls in England and Wales are becoming pregnant.
Ironically, from 2001 to 2003 London had the highest pregnancy rate for this age group of all England's government regions, at 10 per 1,000.
The southeast London rate of 13.6 per 1,000 was the highest in England and was only topped by Blaenau Gwent in Wales, where 14.5 per 1,000 under-16s became pregnant.
Dr Eileen Munro, reader in social policy at the London School of Economics, condemned the protocol as "completely histrionic", while Jan Barlow, chief executive of sexual health charity Brook, said it "goes against everything we believe in".
The most contentious issue is that the Metropolitan Police will hold information it receives on young people aged 13 to 15 as intelligence, even if after discussions with professionals they decide no crime has taken place.
Barlow also expressed concern that the protocol says police and social services should be informed of all cases where an under-13 is believed to be involved in penetrative sex.
She claimed young people would be deterred from seeking advice if they thought "the minute you walk through the door someone is going to report you to the police".
The London protocol is an interim arrangement while national guidance is drawn up to meet recommendations made by Sir Michael Bichard in his report into the Soham murders.
A spokesman for the Department for Education and Skills said the Government was "looking at what guidance would best help children's social services and others to safeguard children and to promote their welfare".
It plans to consult publicly on revised guidance later in the year as part of a "broader revision of guidance on safeguarding children".
- See Analysis, p11, and Comment, p15.