Obesity rates have risen from 9.1% in 2014-15 to 9.3% in 2015-16 for children in reception and from 19.1% to 19.8% for those in year 6, the data reveals.
Responsible statistician, Paul Niblett, said: "This report is a valuable source of information for parents, policy makers and health professionals and these findings show where improvements to children's health can be made."
The report also revealed how obesity varies by local authority. Richmond upon Thames had the lowest figure for reception at 5.1%, compared to 14.7% in Middlesbrough, which had the highest.
Richmond upon Thames also had the lowest obesity prevalence in year 6 with 11.0% and Barking and Dagenham had the highest with 28.5%.
Obesity prevalence for children in reception living in the most deprived areas (12.5%) was more than double that of those living in the least deprived areas (5.5%).
The National Child Measurement Programme measures the height and weight of over one million children in England annually and provides data on which reception and year 6 children are underweight, healthy weight, overweight or obese.