More than 6,000 adults and children took part in the Scottish Household Survey, which offers a snapshot of the health of the population through issues such as smoking, diet and exercise.
It found that the average Scottish child ate just 2.7 daily portions of fruit and vegetables, while 7 per cent did not eat any greens at all.
Fewer children are doing enough exercise since the Commonwealth Games in 2014, as the proportion doing more than the recommended 75 minutes of vigorous exercise per week fell from 76 per cent to 73 per cent last year.
Children were significantly more likely to do enough excercise if their mother was also active, as 78 per cent met the recommendations if their mother also did, compared to 68 per cent if she did not.
Top doctors said the revelations around children’s diets and exercise was “disappointing” as rising obesity levels place further strain on NHS resources.
Jill Vickerman, national director of BMA Scotland said: “It is disappointing to see a downturn both in the percentage of children meeting the guidelines for daily physical activity and the percentage eating five portions of fruit and veg each day.
“We believe that giving all primary school children a portion of fruit or veg each day could help encourage them to start making healthy food choices.”
The doctors union called on the Scottish Government to make sports and leisure activities more affordable to target children from areas of greater deprivation.
Dr Steve Turner, the Royal College of Paediatrics and Child Health’s Officer for Scotland, said: “It’s widely known that healthy children are much more likely to develop into healthy adults.
“At a time where 28 percent of Scottish children are overweight or obese – this compares to just over a fifth of five year olds in England – it is worrying that only 12 percent of children are reported to be eating five portions of fruit and vegetables every day and the number meeting the recommended exercise guidelines has fallen to 73 per cent.
“Creating safer environments and continuing to promote healthy eating will undoubtedly further improve the health of our nation.”
Critics suggested that many areas of public health have remained static, as the report itself said “overall, average levels of wellbeing for adults have changed little since 2008”.
The number of adults doing the recommended levels of exercise per week has remained around 63 per cent since 2012, despite attempts to get the population more active and to build on the legacy of the 2014 Glasgow Games.
Conservative sport spokesman Brian Whittle said: “Nothing like enough is changing – people aren’t eating more healthily, they’re not doing more exercise, and thousands are suffering as a result.”
Only a fifth of adults ate five portions of fruit and vegetables a day, while 11 per cent did not consume any, showing little change since 2003.
Concerning figures show the average waist size has risen by 3 cm since 2003, while 65 per cent of adults in Scotland are overweight, including 29 per cent who are obese. This figure has been relatively stable since 2008.
The proportion of men with a waist circumference larger than 102cm increased from 28 per cent in 2003 to 37 per cent in 2014/2015, while the number of women with a waist circumference greater than 88cm increased from 39 per cent to 52 per cent over the same period.
Doctors would classify 28 per cent of men and 32 per cent of women as being at a “very high risk level” because of their weight.
Labour health spokesman Anas Sarwar said: “We still face the same challenges in obesity, alcohol and smoking as we did ten years ago with little progress.
“We also know that if you come from a poorer background you are more likely to be in poorer health.
“That is why we need to tackle the root causes of inequality in our communities and that includes stopping the cuts to vital public services that impact most on the poorest and most vulnerable in our society.”
Improvements have been made in some areas as nearly three-quarters of boys were found to be a healthy weight in 2015, up from 63 per cent in 2011, while the number of girls in the category was 70 per cent, which has remained steady since 1998.
Public health minister Aileen Campbell said: “I recognise we have much more work to do to improve Scotland’s public health. Many of these indicators are static, or not improving as quickly as we want.
“This government is committed to bringing forward new strategies for obesity, mental health, oral health and alcohol.
“We also remain committed to introducing minimum unit pricing to tackle the damage which high strength low cost alcohol causes in our communities.”