John Stevenson, secretary of Unison's Edinburgh branch, said the proposed establishment of a new investigative team comprising social workers and police was the wrong approach, and advocated closer links with health instead.
He was also worried that the plan would divert resources away from existing child protection services.
The eight-strong team will investigate abuse allegations and is likely to start work next year.
Christina Burnett, operations manager for children and families at the council, said staff were "rightly" worried that the project could take resources away at a time when the department is suffering from staff shortages.
But she said there would be consultation over the next few months to "make sure it fits with services on the ground".
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