He said that architects must be given freedom to innovate and rejected calls to tone down designs following criticisms over the cost and suitability of recent efforts. He also said criticism of the cost of new schools - the bill for one academy is expected to top pound;38 million - was unjustified because the up-front expenses will cut maintenance costs.
The comments by Mr Bowker, chief executive of Partnership for Schools, the agency set up to deliver the Government's pound;40 billion Building Schools for the Future programme, appear to be at odds with those made by a senior adviser to the Prime Minister.
Sir Cyril Taylor, chair of the Specialist Schools and Academies Trust, said in an interview last month that no more "glass palaces" would be built because they are unfit for pupils and teachers.
He singled out the pound;31m Bexley business academy, Kent, designed by Lord Norman Foster, for particular criticism, saying its glass-fronted classrooms were "hot in the summer, freezing in the winter".
Sir Cyril described the construction of some of the existing 27 academies as a "nightmare" and said the remaining 173 academies being planned, which will be aligned to the BSF programme, should be built using a series of "standard designs".
But in his first interview since being appointed head of Partnership for Schools six months ago, Mr Bowker, former chairman of the Strategic Rail Authority, said: "We are building learning environments that are going to last for a very long time, so it has got to be madness to do that on the cheap. We must grab the opportunity to design these things properly with an eye to the future, to flexibility and to creating an inspirational place to learn."
He said most new schools would cost between pound;10m-pound;20m, much less than the bill for some of the new academies, at least six of which cost more than pound;30m.
A Newcastle university study last year said that "fancy classrooms" were a waste of money.
"Anyone who says there is no connection between educational outcome and working environment needs to come with me and I'll show them schools where the water coming down the ceiling is competing with the damp coming up from the floor," Mr Bowker said. "Then tell me that's an inspirational place to work."