The £600 million pound programme was introduced with much fanfare in 2014 by Nick Clegg, who then was deputy prime minister, as a way to improve academic achievement.
However, the new data also revealed the expensive project, which replaced packed lunches with hot meals for all pupils in the first three years of primary school, is failing to significantly improve grades.
New analysis of tens of thousands of children revealed the policy has had limited impact on both making children healthier and boosting their grades, as the scheme was accused of being pricey political posturing.
Politicians had pointed to previous studies that showed that students who had proper meals for lunch were up to two months ahead in their worked compared to those who ate sandwiches and junk food.
The initiative even received the endorsement of Jamie Oliver, who had joined warnings that the obesity crisis would only get worse if the free school meals were to be scrapped.
But new figures, which were obtained by the Mail on Sunday, for two London boroughs – Newham and Islington – showed claims could have been overstated.
The NHS figures showed that 24.7 per cent of pupils who left Newham primaries in 2011 were classed as obese. But for those who left last year and had benefited from five years of free meals, the figured had increased to 27.4 per cent.
In Islington the figure rose to 22.8 per cent from 21.8 per cent in the same time period.
The two "pioneer" boroughs also made limited impact when it came to boosting students’ grades, compared to the London average.
This was assessed by the results of national English and maths tests.
Alan Smithers, director of the Centre for Education and Employment Research at Buckingham University, said:
“The Government's free meals scheme is expensive gesture politics. In these straitened times, the money would be much better spent on education itself.
“There is no evidence of any impact on obesity, nor would much be expected given everything involved in a child’s weight.
“Children spend a relatively small part of their lives at school, so any obesity will be down to their whole way of life with their families, not just those few hours in school.”
Richard Watts, Islington Council leader, said: "Teachers tell us that children's behaviour and concentration have improved and Islington's SATs results are increasing slightly faster than the London and national average."
A spokesman for the Department for Education said: “About 1.3 million more children are enjoying a free, nutritious meal, saving families hundreds of pounds, and, along with our new School Food Standards, establishing healthy eating habits for life.”