A school in Surrey was forced to pay Pounds 16,000 in penalties because it demanded that building work was stopped while pupils were taking their GCSEs. Chessington Community College paid the money to avoid disruption to candidates from power drilling next to the school hall where they were sitting exams.
The money was taken from the Pounds 27 million Chessington was given for a complete rebuild. It is a pathfinder school - handed the cash directly to manage the building programme itself - but it will have to claw back the amount as furniture and fixtures are installed for this summer's completion.
David Kemp, the headteacher, said he did not blame the building company for imposing the penalty, but added that it was just one of many problems that senior staff are left to deal with on their own when managing projects of this type.
"During 2007, the builders were doing piling work, which involved huge drilling machines," Mr Kemp said. "I had to stop them because the only facility I had was the school hall adjacent to where all the work was taking place.
"To avoid similar costs last year, we were forced to hold the exams off site. At one point we were looking at a local Holiday Inn."
He added: "Ensuring quality of teaching and learning is difficult at the best of times, but trying to manage it during a major build is a constant job."
Mr Kemp feels that the sheer complexity of the project and having to make all the decisions alone means there is a temptation to "revert to type", rather than build a school for the future. "All design decisions and all functional decisions are down to you," he said. "We didn't quite revert to 'square classrooms' - but certainly our flexibility was reduced."
The news comes just two weeks after a National Audit Office report on the Building Schools for the Future programme stated that school leaders and senior staff were placed under "considerable pressure" and often felt isolated when it came to managing building projects.
The National Association of Head Teachers said that more should be done to provide support to heads overseeing big projects.
Clarissa Williams, president of the association, told The TES: "The schools have to fit in with the building timetable. The disruptions can go on for anything up to three or four years, and this can have an enormous impact on teachers and on the achievement of the pupils."
A Department for Children, Schools and Families spokesman said: "When local authorities were invited to take up the One School Pathfinder offer it was made very clear that the allocation, which is based on a standard cost calculator, was finite and that the local authority and school must work within that allocation or supplement it from other sources.
"This is a matter for the school and their local authority to resolve locally."