The subsidy costs £5m a year
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Ministers have said the government will continue to subsidise milk in England's primary schools, together with the EU.
They had been urged to reconsider the annual £1.5m subsidy after a study which said the milk could be bought more cheaply in supermarkets.
Parents usually pay the shortfall between the subsidies and the actual cost.
Ministers say continuing the subsidy will support efforts to make school meals more healthy.
There had been a question mark over the government subsidy after a report for the government by London Economics which said the scheme was inefficient.
The average price schools charged parents for subsidised milk - 11.4p for a third of a pint - exceeded the supermarket price for milk which was not subsidised - 8.4 to 10p.
The report was comissioned by the Department for Environment, Food and Rural Affairs, which has announced that the subsidy will stay.
Schools Minister Jacqui Smith said: "I am delighted that milk subsidies will continue. This will complement our work to effect no less than a transformation in the health content of school meals and undo decades of neglect".
The EU subsidy on school milk was reduced in 2000, to just under £6m.
Since January 2001 the government has provided national aid to supplement the EU subsidy in England, funded jointly by the Department for Environment, Food and Rural Affairs, the Department for Education and Skills and the Department of Health.
The Welsh Assembly adds to the EU subsidy to make milk available free to children in reception classes and the first two years of primary education.
In England, new government recommendations mean that from September, the only drinks available in vending machines in secondary schools should be milk, water or fruit juice.