Four in ten (39%) primary school pupils in England are eating school meals but only 35% of secondary pupils, figures from the School Food Trust show.
The figures show a small rise in take-up, of less than one percentage point.
A target to increase the take-up of school meals by 10% by this autumn will now be missed, but the School Food Trust called the results "pleasing".
The figures for this year were based on a much larger sample of local authorities and schools.
Results from those surveyed this year and last show a rise of 0.1% of primary school pupils eating school meals, and a rise of 0.5% of secondary school pupils.
Take-up of secondary school meals in Scotland has dropped by 10% in the last five years, recent figures show.
145 local authorities provided results for primary schools, and 139 for secondary schools, out of a total of 152 local authorities in England.
Former schools minister Jim Knight said in a parliamentary answer in 2007: "Increasing take-up of school lunches is a priority for this department and for the School Food Trust (SFT).
"The SFT has a target to increase take-up of school lunches from a 2005-06 baseline by four percentage points by March 2008, and by 10 percentage points by autumn 2009."
But Prue Leith, chair of the School Food Trust, was encouraged by the results: "We now have a genuine picture of take up across the country and we can see that real progress is being made the length and breadth of England," she said.
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"I am heartened that take up has increased slightly in primary schools following the introduction of new nutrient-based standards.
"It is particularly pleasing that secondary schools have turned the corner."
But the School Food Trust admitted the government had set them a "very tough" target.
Figures published in July 2008 from the SFT showed a modest rise among primary school pupils.
In 2007-08 the proportion eating school dinners rose by 2.3% to 43.6% of pupils, based on a different and smaller sample of local authorities and schools.
This year, local authorities were required to provide information for all their schools, not just those they catered for themselves.
It appears secondary school pupils are still more likely to be tempted by local shop food and shun healthy options.
The proportion of secondary school pupils eating in the school canteen declined by 0.5% in the school year 2007-08.
But this was a much smaller fall than the previous year, when it declined by 5%.
In Scotland, 39% of secondary school pupils now eat in school - but five years ago the figure was 49%.
Again there has been a rise among primary pupils.
The last time school meal take-up increased in England was in 2004 - the year before TV chef Jamie Oliver highlighted the poor quality of some school dinners and began a campaign to improve them.
New guidelines on healthy eating in schools were introduced by the Westminster government from September 2006 and standards for vending machines, breakfast clubs and tuck shops came into force a year later.
There are a number of reasons why the government has missed its target - including the rushed introduction of new food standards
David Laws, Liberal Democrats
Last year, strict nutrition content guidelines for primary schools were introduced, and they will be extended to secondary schools from this September.
School caterers have warned that choice will become a casualty of the new guidelines, as they say it is so difficult to create meals which adhere to the rules.
The Liberal Democrat spokesman for Children, Schools and Families, David Laws, said:
"We now know that barely a third of secondary school pupils are eating school meals.
"There are a number of reasons why the government has missed its target - including the rushed introduction of new food standards, before the groundwork had been done to ensure children will eat the new healthier option.
"The government stands little chance in meeting its targets unless there is both more investment in the school meals service and a massive change in expectations."
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