Study lead author Dr Katherine Black said that when insufficient energy intake is combined with exercise, the body acts to conserve energy through hormonal adaptations, which end up harming health.
"Physical activity, sport and exercise are undoubtedly an important part of a healthy lifestyle. However, when energy expenditure during exercise significantly exceeds energy intake this can cause problems, particularly for bone health and reproductive function," Black said.
Women in the survey were non-elite athletes who did at least 150 minutes of moderate intensity physical activity per week or 75 minutes of vigorous intensity physical activity, or an equivalent combination.
For every one hour increase in exercise a week, there was a significant increase in the likelihood of being at risk of low energy availability (LEA), the researchers found.
There was also a significant association between the number of days off training because of injury and the risk of LEA, suggesting that injuries are linked with LEA risk.
"Given the high proportion of recreational athletes at risk of LEA, the links we have seen with injury, and previous research showing the negative long-term health consequences, we believe is important to raise awareness of LEA and its potential serious health consequences," said Black.
"However, we also need to encourage New Zealand recreational exercisers to continue taking part in physical activity as the health benefits are well established. It is about finding the correct balance between physical activity, energy intake and well-being."
Black told the Herald that women whose BMI is in the overweight or obese category and who are exercising to lose weight, could suffer from low energy availability.
"What I would suggest is that they continue to exercise but ensure that they don't excessively restrict their food intakes.
"Gradual weight loss around 0.5-1kg per week is what is recommended. Severe food restrictions, skipping meals or limiting intakes is probably when you would see issues.
"If someone is overweight or obese then we would suggest sensible weight loss, which includes exercise because of the benefits on their long-term health."
Black said it was difficult to assess a person's energy intake and expenditure.
"Therefore instead we looked at the symptoms related to low energy availability such as menstrual status and gastrointestinal symptoms such as constipation to determine if an individual was at risk of low energy availability.
"Previous research has used controlled laboratory studies which manipulated energy intakes and energy expenditure. They have shown that when energy availability was below 30kcal/kg [kilocalories per kilogram of] lean body mass, alterations in the reproductive hormones were seen. Someone with an energy-balanced diet would have an energy availability of around 45 kcal/kg lean body mass."
The findings are published in the International Journal of Sport, Nutrition and Exercise Metabolism.