The Sure Start programme was hailed as a positive step for society as it aimed to break open the poverty trap in the country's poorest areas when it was launched four years ago.
But the first large-scale study of the scheme has revealed that the most disadvantaged groups fare worse in Sure Start areas than similar parents elsewhere.
The study looked at groups of nine-month-old children and three-year-olds.
It found that in Sure Start areas three-year-olds born to teenage mothers scored lower for verbal ability and social competence and had more behavioural problems. The verbal ability of three-year-old children of single parents and unemployed parents was also relatively poor.
Although these disadvantages in early development were small and affected around 15 per cent of the sample population, the researchers said the findings were too significant to be ignored.
Professor Edward Melhuish, of London's Birkbeck college, who wrote the report, said: "We are talking about an important minority. If you look at the later costs to the education system, the criminal justice system, social services... these are the groups which use a disproportionate amount of money."
However, there were some positive results in Sure Start areas for less deprived families where children scored higher for verbal ability and parents were reported to be less inclined to shout at or slap children.
Professor Melhuish said the overall findings had surprised researchers and that future results would give a more realistic measure of the programme's impact. He called for more highly trained staff, possibly nurses, to be brought in to target the most deprived families.
"The Sure Start programmes have to get their act together in terms of reaching that (most deprived) population," Professor Melhuish said.
Sure Start, which was launched in 260 communities, is aimed at children under the age of four living in disadvantaged areas. It comprises children's centres, child-oriented health services, and parent and child facilities including day centres and creches.
Ruth Kelly, Education Secretary, said that Sure Start has several different models and the most successful need to be adopted elsewhere.