Fitness was measured on an exercise cycle among members of the Dunedin Multidisciplinary Health and Development Study when they were aged 15 in 1986/87.
The same fitness test was completed on 343 of their 15-year-old children between 2007 and 2015.
The decline has been accompanied by an increase in body weight to keep up with global trends of increasing body weight among children and young people.
Researcher Dr Helena McAnally said female fitness was notable lower with fitness test scores around 25 per cent lower than their mother's generation.
"It is well recognised that girls become less physically active earlier in adolescence, and this may be why their fitness levels were so much lower.
"We know fitness in adolescent tracks into adulthood and so these changes may have important long-term consequences for health and wellbeing," Dr McAnally said.
Study leader Professor Bob Hancox said the rise of children being overweight and having obesity was well documented but there is little research on changes of fitness.
"Our study is unusual in that we have measured fitness using the same technique in two generations of New Zealanders.
"The findings support many people's perception that young people are less active and fit than their previous generations," Professor Hancox said.
The study measured fitness using a cycle test which is less likely to be influenced by changes in body weight, rather than running tests.
If they were required to run they would have to carry their own weight, rather than sitting on a bicycle seat.
Findings of reduced fitness in this research are not likely to be explained by increases in body weight.
