It argues that the introduction of fresh healthy food has actually helped to reverse the downward trend in school dinner uptake.
"Contrary to the BBC's findings, we've seen that schools that have involved pupils and parents in changing meals for the better - and switched to ingredients that are fresh, local and where possible organic - are actually seeing uptake rise, not decline," said Soil Association food for life coordinator Joanna Collins.
"This is not rocket science, as schools all over the country are proving."
Collins' comments came in response to an article on yesterday's BBC's news homepage, which claimed that out 59 local authorities that responded to a survey, 35 (59 per cent) said the number of pupils eating dinners had gone down.
Of those, 71 per cent agreed Jamie Oliver's healthy meals campaign was a reason. Jamie Oliver, a celebrity chef in the UK, has been vigorously and visibly campaigning to improve the content of school dinners.
But the Soil Association argues that schools following the Soil Association's Food for Life programme have bucked the national trend on uptake.
"St Aidan's Church of England High School in Harrogate made the switch to fresh, locally sourced food - with homemade chips limited to once a week - back in 2002," said the association.
"Despite a 5 per cent price rise, take-up rose from 30 per cent to over 90 per cent."
In Essex, the Soil Association said that 25 schools working to serve up wholesome, local and organic school meals have seen an average increase in uptake of school meals of 38 per cent in just one month. And in Bradford, the amount spent on school meal ingredients per child has risen by 14p since May 2005 to 60p.
The Soil Association's Food for Life programme aims to provide food that meets the nutrition targets set by the Caroline Walker Trust and the School Meals Review Panel. It states that 75 per cent of all foods consumed should be made from unprocessed ingredients, and that at least 50 per cent by weight of meal ingredients should be sourced from the local region (50 mile radius or the proximity principle applies).
The School Food Trust - set up by the government in 2005 to improve school food predicted that the downturn would be temporary.
Chief executive Judy Hargadon told the BBC that she "expected there to be a bit of a downturn; children are going to have to get used to eating more healthy food at school and it takes a while for them to get used to that.
"Some schools have however proved that it can be done and that children really enjoy eating healthy food, so our job is to help people get through this dip."
Of the 59 authorities that responded to the BBC survey, six had more pupils taking meals, eight reported no change and 10 said the changes were not applicable. Half said a factor in the decline was the restrictions imposed on vending machines, while some said the prolonged warm weather had had an effect.
Overall the decline was just 5.8 per cent, though individual areas had seen decreases of as much as 30 per cent. Declining pupil take-up of school meals has also been reported in Scotland and Wales, following drives to improve the quality.