After-school clubs offering homework, chess and activity classes are being shut down in some of the poorest parts of the country, while the children of middle-class parents, who can afford to subsidise them, are reaping all the benefits of the scheme.
By 2010, the Government expects all schools to be "extended schools", offering quality childcare, catch-up classes and sport to all pupils outside formal school hours.
Gordon Brown, in his first major speech on education last week, praised the clubs for their impact on raising standards.
And research by the Joseph Rowntree Foundation has found that extended schools give poorer children access to the wider range of experiences often enjoyed by children from better-off families.
However, services in deprived and rural areas are struggling to survive. More than 100 have closed this term alone, with a further 50 expected to follow by the end of the year.
Schoolfriend etc, the UK's largest operator of after-school clubs, said there was a "great divide" between government rhetoric and reality.
Money is available to set up the schemes, but they are expected to become self-financing through parents paying fees.
Stephen Argent, co-founder of Schoolfriend etc, said this policy had led to councils funding clubs in prosperous suburbs where they know middle-class parents can afford to use them. In deprived and rural areas, where take-up is slower, councils are refusing to provide the on-going funding required, he said.
"We are very upset about the situation. The Government will fail to meet its goal unless this is addressed immediately," he said.
Ministers estimated that 7,000 schools were offering extended services in September. It has committed pound;1.3 billion to fund them over the next three years. A spokesman for the Department for Children, Schools and Families said that financial support could be given to extended school services facing closure, but that it "should generally only be given to providers who are capable of becoming sustainable".
Mr Argent met senior Downing Street officials last week and is due to meet Ed Balls, schools secretary, later this month.
Mr Argent is urging the Government to change the rules on working tax credits, so that parents training for a job or looking for work can claim back the cost of after-school clubs.
Salhouse Primary School, a rural school near Norwich, is at risk of losing its services because it cannot consistently attract enough pupils.
Karen Dukes, its headteacher, said: "I'm strongly of the opinion that we should be here for parents as and when they need us. But there is no extra money for it."