Gove suggested on 2 June that funding was inefficient for a programme that has drawn both praise and criticism for standards of architecture and landscape design.
The MP, a vocal critic of BSF, has previously suggested architects "cream" off fat fees from the biggest ever schools building investment scheme, launched by Labour.
RIBA President Ruth Reed said: "Intelligent use of space can foster different ways of learning and directly affect behaviour and attainment.
"This is not to say Building Schools for the Future has not wasted money; the method for procuring the buildings is inefficient and takes too long."
Losing contractors wasted many millions of pounds per failed bid, she said.
"We appreciate the new coalition has a different approach to schools and we are operating under financially constrained time.
"But purporting a myth that architects were part of the problem is missing the real point - architects have made a key contribution towards making schools a better environment."