The Association of Directors of Social Services' finding is bad news for the Government, which wants all local authorities to establish a single director of children's services within the next four years.
The survey of 95 social services directors shows they have fears about the changes heralded by the Government's Children Bill.
Nearly 55 per cent said they felt merging education and social care departments would not "improve their ability to protect children from harm". Only a third thought it would improve support.
They were also unhappy that education directors might beat them to become director of children's services. In authorities where merger is planned, more than 90 per cent said they would consider quitting if their education counterpart got the job. A majority said they would be uncomfortable reporting to their education director.
Andrew Cozens, president of the ADSS, said fears may have been overstated because the survey was carried out at a time of uncertainty shortly before the publication of the Children Bill last month.
The Association of Chief Education Officers last month renamed itself the Association of Directors of Education and Children's Services to reflect the changes in local authorities.
David Hawker, vice-chair of ADECS, is director of children's services for Brighton and Hove, which combined its social care and education departments two years ago.
He said it was no surprise that local authority staff would prefer the children's services director to be from their department, but that it was not a significant problem.
"My background is in education but I have a senior team with a range of professional experience so we can ensure we keep both the school standards and the child protection agendas strong," he added.