Writing in this week's TES Scotland, Sandy Wilson, who was head of education and lifelong learning in Clackmannanshire, accuses HMIE of a "cavalier" approach in using different bases for its statistical analysis of the education services in Clackmannanshire and East Ayrshire.
Mr Wilson said that this was "at the very least careless or incompetent".
He added: "The outcome is certainly less than impressive and is one which undermines any residual confidence I had in HMIE's capacity to understand, far less report objectively on, the performance of education authorities."
Mr Wilson says he is not trying to disparage East Ayrshire's performance or elevate that of his former authority. HMIE's analysis was that the impact of Clackmannanshire on learners and its record of continuous improvement and performance was good and adequate; East Ayrshire scored very good and good.
The reports on the two councils were part of the second cycle of education authority inspections known as INEA (inspection of education authorities).
A spokesperson for HMIE said the exercises in Clackmannanshire and East Ayrshire took the form of extended pilot inspections which were specifically designed to trial some of the methodologies for the new inspections. "This meant that different approaches were trialled in each of the inspections, and these variations were exactly what the pilot was for,"
the spokesperson said. She added: "Neither of the pilot inspection reports will be used for comparison for the next cycle of inspections and they were not published in the usual way. The nature and scope of the published report was also part of the trials and was intended to be different in each of the two pilot areas."