Under the proposed restructure she will not be replaced; instead children and education services teams will "report to other directors".
A month-long consultation on the proposed restructure has launched and is set to reduce the number of senior managers from 17 to 12. The move is set to save £500,000 a year.
Ruth Bagley, Slough Borough Council’s chief executive, said the decision to axe Pyper’s role comes amid a reduction in the council’s involvement in education caused by the government’s free schools and academies drive.
She said: "In particular in the education arena, government policies are causing many changes very quickly, with schools rapidly become academies and local authority involvement becoming much less.
"The proposal is designed to reflect the changes taking place, to reduce costs and also maintain the capacity to face and adapt to future change."
An Ofsted report into child protection procedures released last June was highly critical of the council.
It found inadequate practice in risk assessment, care planning and managerial oversight. Inspectors found a "systematic failure" among some managers and independent reviewing officers, and said there was a lack of contingency planning for children subject to child protection plans over a period of months.
