NHS managers have defended giving girls as young as 13 contraceptive implants in school in an attempt to combat teenage pregnancies.
She told the Southern Daily Echo that giving the girl the 4cm device without her knowledge, or that of her GP, between lessons was "morally wrong".
"I feel really angry about this. I agree that teaching teenagers about sexual health and contraception is very important but this is a step too far.
"I have spoken to a lot of parents at the school and they were horrified to find out this was happening."
The mother, who did not want to be named, claimed her daughter received no follow-up appointments and had suffered mood swings, depression and cut off contact with her friends.
The schools which allowed the scheme in Southampton were not told who had sought advice due to patient confidentiality rules.
Britain has one of the highest rates of underage pregnancy in Europe, prompting the then Labour government to launch a teenage pregnancy strategy in 1999 to combat the problem.
Best practice guidance from the Department of Health states: "Doctors and health professionals have a duty of care and a duty of confidentiality to all patients, including under-16s.
"This guidance applies to the provision of advice and treatment on contraception, sexual and reproductive health, including abortion."
In a statement, Solent NHS Trust said the scheme, in place since 2009, had cut under-16 pregnancies in the city.
"NHS Southampton is committed to ensuring local young people are able to access clinically appropriate sexual health support, advice and treatment to help them avoid unwanted pregnancies and protect themselves from sexually transmitted infections.
"One element of this is commissioning a sexual health service for young people that is provided in nine secondary schools and all three colleges across the city.
"The service is provided by trained staff and includes offering information, advice and support to students as well as chlamydia screening, condom distribution, pregnancy testing, providing a range of contraception methods and referral to other services.
"Since the service was introduced there has been a reduction in the number of under- 16-year-olds who have become pregnant."
A Department of Health spokesman said: "Young people should think carefully before having sex. If they decide the time is right, they should talk to an adult about contraception.
"The health professional must always encourage a young person to talk to their parents or another trusted adult about their sexual health. The health professional should be fully satisfied that the young person understands all the issues before they prescribe any contraceptive.
"It's a matter for schools - in consultation with parents, governors and local health services - to decide whether to have a sexual health service."