The area-based grant funds teenage pregnancy work, Care Matters and positive activities among others.
Birmingham, one of the larger authorities, is facing a £7.5m cut from the DfE area-based grant, while Essex Council is losing more than £6m. Smaller authority Westminster Council in London is facing a £1.5m cut.
Councillor Paul Dimoldenberg, leader of the Labour group in Westminster, said his authority could not afford to lose £1.5m without damaging frontline services.
"The [government] said these initial cuts would be about reducing waste," he said. "But now we find out they have targeted children for the most savage cuts."
Andrew Cozens, strategic adviser for children's services at the Improvement and Development Agency, warned that the most efficient councils would be worst hit, as they have less scope to cut waste.
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