Hillingdon Council, Liverpool City Council, Leeds City Council and Norfolk County Council sought a judicial review after claiming that the raised fees could put funding for other children's services at risk.
They said that from May 2008 local authorities have had to cope with a 2,500 per cent increase in court costs for judicial care proceedings.
But today (6 November) three High Court judges dismissed the application.
Wes Cuell, acting chief executive of the NSPCC, said he hoped that the court was correct in its assessment that vulnerable children will not be at risk under the new court fees regime.
"We remain certain that taking this matter to judicial review was the right course of action," Cuell said. " We were pleased to be able to draw our concerns to the attention of the court and we support the local councils' decision to apply for the review."
A joint statement from Hillingdon Council, Liverpool City Council, Leeds City Council and Norfolk County Council, said: "This is a disappointing result although we stand by our decision to take this action, as it highlights our concerns about the way in which these costs were imposed on local authorities and ultimately the local tax payers."
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