Speaking at the Children, Schools and Families Select Committee last week, Sunand Prasad said that construction companies could lose between £5m and £7m when they bid for a BSF project, which then gets turned down.
There are usually at least three bidders for any one BSF project, meaning that more than £10m is wasted on unused bids every time a BSF school is built.
He said: "That money has to come from somewhere, and ultimately, the bidders who have risked that money will get it back from the public sector in the long term."
At present, bidders compete based on the amount of risk they can afford to take, instead of competing based on the value for money they can offer, Prasad warned.
He said: "The biggest scope for savings for the public purse right now would be the streamlining of the procurement method to reduce bid costs."
Ian Fordham, deputy chief executive at the British Council for School Environments, said the BSF procurement process could be improved by focusing on local authorities' skills.
The National Audit Office is due to report on how efficiently the BSF programme is using public money on 12 February.
Barry Sheerman, chair of the Children, Schools and Families Select Committee, promised he would look into how to reduce the costs of bidding for projects.
