The Beyond the School Gate scheme aims to promote healthy eating for children when they are outside school by encouraging shopkeepers to think about the food they are selling to youngsters.
The project is also promoting ways to encourage children to stay on school premises at lunchtime and eat a healthy meal.
It comes as research carried out for the project by Young Scot found that more than half of secondary school pupils buy lunch outside school at least once a week.
Of the 938 young people who responded, more than 70% had at least four food outlets in the immediate vicinity of their school. The most common shops visited were large supermarkets, small convenience stores and bakeries.
Public health minister Michael Matheson launched the scheme in Glasgow during a visit to Eastbank Academy.
He said: "We have made excellent progress in improving the standard and nutrition of school meals in Scotland.
"However, the evidence shows that many children are simply not staying to eat these meals.
"We are fighting a battle against obesity in Scotland and we know that if children eat unhealthily in their teenage years it's a habit that can be hard to break.
"That's why this is a battle we want to take beyond the school gates. This initiative looks at how we can encourage children to choose healthier options both inside and outside school."
Under the project, which is backed by council body Cosla and the Scottish Grocers' Federation, schools are being offered advice on how to encourage pupils to stay on-site at lunchtime.
Suggested ways of achieving this goal include offering better cafes and more appealing food and drink.
Local shops are being given tips on how to increase the sale of healthier options, such as by using marketing, promotions and incentives.
John Drummond, of the Scottish Grocers' Federation, said of the project: "It is having a real impact in our communities and shows the highly active role that retailers play in offering healthy eating choices and promoting healthy foods, particularly fresh fruit and vegetables."
Peter Johnston, Cosla's health and wellbeing spokesman, said: "Councils have done much to improve the food on offer within our schools in recent years and are working hard to encourage more pupils to take advantage of this more often."