It is feared that the financial loss to the 1300-pupil Hermitage Academy in Helensburgh will threaten the sustainability of the school meals provision.
It is estimated the opening of the 300th Waitrose store close to the school, which had been seen as the ultimate badge of endorsement, has cost the academy nearly £35,000 since it opened. Argyll and Bute Council, which has confirmed the depths of the financial loss, insists that there remains a "healthy demand" for school meals, that it "is sustainable and it will be maintained".
The Helensburgh Waitrose branch, the sixth in Scotland, opened in October last year, creating around 200 new jobs in the area. It has 25,000 square feet of retail space, a coffee shop, petrol station and 180 car park spaces.
But there has been growing concern that hundreds of pupils are spending their money in the Waitrose store instead of taking school meals.
James Robb, a former council leader and Hermitage Academy Parent Council member, said the concerns about the shop being just a three-minute walk from the school have been realised with hundreds of pupils using the store.
He said: "Helensburgh's first out of town supermarket has an enthusiastic following and is a huge success.
"Almost half the pupils now choose Waitrose instead of school meals. The effects on social inclusion, learning and health are complex and any mitigation will require co-operation between the school and the supermarket.
"The financial loss to the school of £80,000 per year, which threatens the sustainability of school meal provision, is simple and quantifiable which any ethical, responsible and highly profitable business should accept as its responsibility to make good." He said 225 pupils in their first year are "strongly encouraged" to stay within the school grounds and this has "good compliance".
Darrel Hendrie, convener of Helensburgh Community Council, added: "For some children the only hot meal they get a day is a school meal, so it would be a shame if school meals were to finish as a result of this."
Council sources have confirmed staff have been attempting to overcome the deficit by running promotions to encourage pupils to remain in the school at lunchtime.
They say the lunches offered in the school canteen meet the standards specified within the Schools (Health Promotion and Nutrition) (Scotland) Act 2007 which sets nutritional guidance for food and drink being served in schools.
It says the canteen does not sell any items such as chocolate or soft drinks, because it breaches the aims of the act.
And when available, snack items are generally lower in fat and salt than would otherwise be available from other outlets, it explains.
Aileen Morton, Argyll and Bute Council's policy lead for education, said the school meals service won a bronze award from the organic campaign group the Soil Association, which was "testament" to the staff's "initiative and efforts".
"Our school catering staff have been working hard to encourage pupils to have lunch in the school canteen, offering special promotions and healthy, attractive food choices," she said.
"Inevitably some pupils choose to buy lunch elsewhere and this is an issue for schools all over the country. Our catering team will continue their efforts to encourage more people to use the school meals service."
Waitrose said it did not wish to comment.