Douglas Osler pointedly underlined the important role local government can play in raising attainment at a time when councils are becoming nervous over Labour's plans to subject education services to HMI scrutiny, and when there is increasing uncertainty over their place under a Scottish parliament.
Following last week's HMI review of the way Standard grade and Higher targets are managed, Mr Osler told The TES Scotland: "Where authorities showed considerable commitment and gave strong leadership, engaging schools in a constructive approach, targets were set which were realistic and challenging.
"Where there was a lack of commitment and leadership, considerable autonomy was given to schools and they used that autonomy to lower targets by more than the agreed one per cent flexibility.
"That is very worrying because it means the challenge for pupils has been lowered. But it also underlines the important role that education authorities can play, with their schools, in raising attainment."
HMI considers that 13 authorities either did not use the leeway of "exceptional circumstances" allowed to vary targets or used them sparingly, a further 13 were found to have broadly acceptable targets although some unacceptable exceptions were claimed, and six set targets which were based on "invalid" circumstances.
There are to be no recriminations, however, and schools will not be ordered to increase their targets following the agreement on flexibility hammered out in bumpy negotiations last year between directors of education and Brian Wilson, the previous Education Minister, to give schools "a sense of ownership".
But the worst offenders will be expected to exceed, not just meet, their targets. In addition, HMI will henceforth pronounce on the appropriateness of targets when inspectors report on schools.
Mr Osler has now sent a letter to the three groups of authorities explaining the findings. The investigation was ordered last September after the Education Minister expressed concern at the approach of some authorities.
"The process must be as rigorous as possible," Helen Liddell said then. But, with an election looming, Mrs Liddell may have decided that high-profile intervention at this time might not be advisable. This was reflected in her reaction to the 5-14 targets.
Although most will be wide of the mark by 2001, she opted for the relaxed comment that "schools are taking the first important steps to improvement".
Criticism of failure by some schools to set realistic targets was therefore left to Mr Osler.
Exceptional circumstances are defined as situations affecting one school but unlikely to affect another, such as the recent Glasgow closures and mergers or a fire. In such cases, targets can be decreased by more than 1 per cent.
Among unacceptable excuses that were used to lower targets schools claimed there was no tradition of pupils achieving five or more Highers, blamed disruption caused by building work, said an excess of boys in a year was likely to drag down performance, or cited a new headteacher or too many probationers.
These excuses are "unacceptable and frankly absurd", Mr Osler said.
The Inspectorate's report found "concern that more demanding targets were potentially demotivating and carried the risk of adverse impact on the school's reputation if they were not met".
HMI was more impressed by authorities and schools that "adopted a stronger approach in the belief that they should commit themselves to 'having a go' - even when the challenge seemed tough - and that no stigma would attach to missing the target in such circumstances".
Despite specific reservations, however, the general conclusion by HMI is that "a good start to setting targets has been made".