They describe "a top-down giving of instructions, delivered in a patronising and sometimes aggressive manner".
The letter to Douglas Osler, head of the Inspectorate, says that the team led by Frank Crawford, the chief inspector in charge of the Audit Unit, failed to answer the heads' questions, especially those relating to small rural schools.
The letter adds: "We found the presentation extremely dull and coldly delivered. For any headteacher who had read the target setting document, much of the morning was a waste of time."
The heads state their commitment to raising attainment levels. But they describe the education system as "ever more centrally directed, and (one) where there is a single set of right answers handed down from above".
Sheena Vannan, headteacher of Philiphaugh Community School, Selkirk, and chair of the association, told the TES Scotland that many of her colleagues had come away "thoroughly demoralised". The HMIs' answers were "pat or political", and heads of small schools had been told that they should deal with targets in their "clusters".
"But how can we do that," Mrs Vannan asked, "when we are responsible for standards in only one school, our own?" Mr Osler wrote back expressing "disappointment" at reaction to the seminar, which had been carefully planned and contained an "extensive" question and answer session. Evaluation forms showed that three-quarters of participants rated the keynote address good or very good, with the workshops described as good or very good by 60 per cent. The question on small schools had not been ignored: the seminar was told a national officer is preparing advice to be available in the autumn.