The problem usually occurred in women with low body-fat levels, causing their periods to stop - the body's way of signalling that it was not healthy enough for a pregnancy.
Career-driven women also developed the disorder as they worked in demanding environments that caused weight loss due to stress, Dr Milsom said.
But the majority of patients were from girls-only schools, where there was a "terribly high rate" of the syndrome.
Dr Milsom said she wanted to differentiate the problem from eating disorders, such as anorexia nervosa, which were "at the other end of the spectrum", but conceded that some of her patients were anorexic.
Some young women were tricky to treat as they preferred to continue being slim and period-free, refusing to recognise the dangers of dieting.
"No one likes the advice to stop your exercise and eat more. One of the things that always comes up is, 'But my friends are the same weight'."
Dr Milsom said she was "astonished at the ignorance" of women told "not to worry" by family and friends when they revealed they weren't menstruating.
One of her in-vitro fertility patients had not menstruated for five years and had not sought medical advice for the issue before visiting her for help to achieve pregnancy.
Dr Milsom said although she did not have figures on how many women developed the disorder, she had seen an increase in the prevalence of the condition, which reflected the stresses of the modern lifestyle.
New Zealand Eating Disorder Specialists director Charles Fishman said high achievement among young women should not be "pathologised", but he believed the pressure to achieve perfection - spoon-fed to teens by the media - could lead to eating disorders.
He warned that although anorexia was rare - it affects an estimated 0.5 per cent of New Zealanders - an absent period was an early warning sign for the eating disorder.
If exercise and control of diet were taking over a patient's life, Dr Fishman said, they should be referred to a specialist.
ALARM BELLS
Warning signs of hypothalamic amenorrhoea:
* Irregular menstrual cycle, or stopped periods.
* Puberty not occurring by the age of 14.
* At-risk group: high achievers.
* Restricting nutrition, overexercising.
* Body Mass Index less than 20.