Mr Balls has appeared to rule out cutting teaching assistant jobs
Millions of pounds of taxpayers' money is being wasted in the Department for Children, Schools and Families, an internal government report suggests.
The report, by former WH Smith chief executive Richard Handover, has been seen by BBC One's Politics Show.
It claims civil servants and head teachers appear to have no idea what value for money means, and calls for 40,000 teaching assistant jobs to go.
Schools Secretary Ed Balls has said £2bn could be cut from his department.
However, last week, he appeared to rule out the sort of job losses proposed by Mr Handover.
In his frank report, Mr Handover states: "Financial efficiency... is not seen as a core responsibility of management at any level."
He described how £50,000 was spent installing three toilets at a primary school - 10 times the required sum, while another spent £35,000 on a £1,000 photocopier.
A DCSF spokesman said Mr Handover was asked last September to conduct a "value for money review" of the department's spending. He concluded his work and handed his report to the Secretary of State in April.
The spokesman said the report was "useful blue-sky thinking", which had already helped the department identify savings that could be made.
But he said Mr Balls had made clear that in some areas he did not agree with Mr Handover's thinking.
He said: "For example, Ed Balls was clear that he did not agree with Mr Handover's view on deprivation funding and will not pre-empt the School Funding Review and that he did not want to see fewer teachers or teaching assistants but rather wanted to keep the extra 40,000 teachers and the extra 120,000 extra teaching assistants."
Mr Balls became the first minister to suggest possible cost-cutting moves last week when he suggested £2bn could be trimmed from the budget.
The number of bureaucrats and senior staff could be reduced without losing front-line staff or affecting the quality of teaching, he suggested.
He also claimed £500m could be saved by comprehensives merging to form federations with a management pool working across several schools.
In response, the National Association of Head Teachers said its members had been forced to deal with increasing amounts of government bureaucracy.
Teachers' unions accepted some reorganisation could be carried out at senior levels but rejected suggestions of job cuts.
The Politics Show is on BBC One at 1100 BST on Sunday.