Jack McConnell, the Finance Minister with responsibility for modernising government, said the charter is intended as a safeguard to ensure accountability.
The charter was drawn up by a working group from the inspectorates chaired by Douglas Osler, the senior chief inspector of schools.
Ministers believe the charter is needed because of the number of bodies carrying out inspections or quality assurance. They also believe there is a need to establish "shared principles" in line with the agenda of "joined-up government." All inspectorates will now customise these principles for their own needs by December.
The charter requires the inspectorates to show independence, openness, impartiality and commitment to continuous improvement. They must also operate a clear complaints procedure.
Inspectors will be expected to "carry out inspections openly and encourage informed comment and criticism from those involved in the process of inspection".
The alleged absence of these qualities fuelled hostility to HMI last weekend at the annual conference of the Educational Institute of Scotland. The union's executive was asked to protect members from HMI "pressure". James Kane from West Dunbartonshire, who moved the motion, said the range and frequency of inspectorate reports have made HMI "the Barbara Cartland of the educational world".
Lesley Donaldson, a Borders delegate, claimed one primary head in her area fel "violated" following an inspection by a three-strong HMI team which lasted five days. The only place she felt secure was in the toilet.
The conference also heard fierce condemnation of the way HMI had pressed ahead with an inspection of Abronhill High in Cumbernauld, despite the murder of a teacher, the death of another and several staff illnesses. No account was taken of the circumstances of the school and these were not mentioned in the final "disgraceful" report, according to Andy Herron, a teacher at Abronhill.
The conference backed the North Lanarkshire motion, which called for inspections to be delayed on compassionate grounds where a school faced "exceptional or tragic circumstances".
The spate of attacks on HMI forced ministers to concede a code of practice for the inspection of schools (but not further education colleges) during the committee stage of the education Bill. This will give ministers wide-ranging powers to issue guidance to HMI, as had already been proposed for the new inspections of education authorities.
Peter Peacock, the Deputy Minister for Children and Education, told the committee in April that it was important the code cleared up "misconceptions" about the role of HMI.
Despite the unprecedentedly frosty relations between the unions and inspectorate, there are also signs of a thaw. A meeting between the two sides in April agreed the outline of an "early warning" system under which schools and the EIS can alert senior inspectors when any HMI acts "outwith agreed practice" in a school - although the inspectorate says this simply formalises existing understandings.