Award-winning architect Fraser said that schools being built through public-private partnership (PPP) have undergone 'catastrophically poor' design.
'The general silence of the building industry on this issue is a disgrace,' he said. 'All know of its fundamental flaws, but there is a river of money flowing from it towards us so we keep schtum.'
Fraser added: 'I have seen nearly 100 of these schools and I saw 27 schools for the Highlands. This is the biggest single financial investment in the built infrastructure of the Highlands and the future of the people - and these schools are catastrophically poor.
'I'm not talking about design as a subjective thing, I'm talking about objective evidence-based design which says we are currently building schools right across the Highlands that will blight the lives of those that will learn in them.'
Fraser said he had been pushing for better design of schools within A&DS for the last two years.
'I've been fighting the cause for two years, and it was only when I realised that nothing was going to happen that I decided to hand my resignation in.'
Fraser's comments will be widely welcomed by architects in Scotland, not least by Alan Dunlop of GM&AD, although Dunlop claims it is a change of tack from Fraser.
Dunlop said: 'I'm happy Fraser has taken this stance but it has taken a while, when some of us have been speaking out about PPP for the last three years - putting our businesses at risk.
'I wrote a column in a national architectural publication last November saying how ineffective A&DS was and how they ignored the big issues like PPP. Fraser responded by saying I was an embarrassment - funny how things change.'