The department last week confirmed 700-800 employees could lose their jobs as part of an "efficiency review".
The Public and Commercial Services Union said: "We remain at best sceptical that the Government can deliver the agenda set out in the Children's Bill and green paper while all this turmoil is going on."
The union has been told the cuts will be made by 2006 and "various directorates have been asked to plan what this could mean for them, including the Children, Young People and Families Directorate".
The union fears the plans may lead to an increased workload for teachers and local authorities. "We're not campaigning for an overstaffed civil service but, if the work needs to be done, who will do it?" said a spokesman.
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