46,000 students will take part in a survey next year, where their Body Mass Index will be scaled and their school bags weighed.
It was also announced that as from next September, children will only be allowed to drink water in schools.
Education Minister Evarist Bartolo and Parliamentary Secretaries Chris Fearne and Chris Agius attended the launch this morning, at St Clare's College Pembroke.
Studies have shown that 25% of children at school entry age in Malta were classified as overweight or obese, they said, adding that over a three-year interval, the percentage of children classified as overweight increased by 33%.
The survey will be the first nationwide BMI school children survey in the EU, and will be used to help healthier development. It was also announced that a priority of Malta's EU Presidency will be to help tackle childhood obesity by coming up with international strategies.
School bags will also be weighed, and in collaboration with the Malta Association of Physiotherapists, a small cohort of students from Form 1 to Form 5 will undergo back pain assessments.
The survey will encompass around 2,300 classes, with 25,149 students in State schools, 15,000 in Church schools and 5,500 in Independent schools.
Physical Education teachers are currently being trained to use the scales and to ensure uniformity in the data captured and information gathered will help guide policy changes.
Parental permission will be required for students to take part and all results will be anonymous.
The study will help create a baseline for all school children, and will help accurately measure small shifts in BMI trends as it will be carried out periodically. In addition, an intervention strategy can be planned and implemented both by the Ministry for Education and the Ministry of Health as part of a national campaign to combat obesity.
Education Minister Evarist Bartolo explained that parents must also help at home, stressing that half an hour of exercise after school is beneficial. He also mentioned the healthy lunchbox campaign and that parents should give their children healthy meals.