According to the report, the teenager had a contraceptive implant inserted when she was 13 with the support of her family.
Three years later, she consulted a nurse at Family Planning about having it removed because she was unhappy with its side effects.
During the appointment, her grandmother and court-appointed guardian contacted Family Planning to advise the teenager did not have the capacity to make the decision to remove the implant, and asked the nurse not to remove it but wait until she could give more information.
But the nurse deemed the patient competent to decide after consulting senior Family Planning staff. She removed the implant and gave the teenager condoms for ongoing contraception.
Health and Disability Commissioner Morag McDowell was critical of the nurse and said she should not have removed the contraception until the issues raised were clarified.
This case showed the need for healthcare providers to understand the impact of neurocognitive impairments like FASD on patients' capacity for decision-making, McDowell said.
"People with such impairments present uniquely, with their own profiles of strengths and impairments.
"As has been seen in this case, individuals may present with subtle impairments that can be overlooked or underappreciated by those providing them with care."
People with FASD may communicate and appear to understand decisions but have difficulty foreseeing the consequences of decisions, she said.
"Each assessment should depend on the nature of the procedure being consented to, and it may be appropriate for providers to defer assessing capacity to a more experienced colleague or provider with relevant specialist expertise."
Her report said Family Planning did not have adequate protocols to deal with the situation of assessing capacity in a young person with intellectual impairment, and its staff had failed to recognise the red flags that should have delayed removing the implant.
McDowell recommended that both Family Planning and the nurse apologise to the teenager and her grandmother, and arrange training on informed consent and assessment of competence.
The nurse was also asked to review the Nursing Council's code of conduct for nurses, especially where it concerns recognising and working within the limits of her competence.