In his resignation letter, which has been sent to all SSBA directors and some former directors and which has been seen by The TES Scotland, Mr Stewart has made a series of extraordinary allegations naming those he says have been engaged in a campaign to ditch Ann Hill, the SSBA's chief executive.
Mrs Hill is seeking severance terms from the organisation she founded. The executive is understood to be willing to consider a redundancy package on the grounds that the association is "winding down" following the recommendations of the Banks report on the future of school boards.
In his letter, Mr Stewart, who is from Glasgow and represented special needs on the 32-person SSBA executive, claims that Mrs Hill's principal antagonists are Gino Satti, the company secretary; Caroline Vass, a representative from East Lothian; and Kathleen Glass, who represents Dumfries and Galloway.
Their actions, Mr Stewart claims, have already led to the departure of John Tierney, the former president, and Jeff Taylor, the previous vice-president, and warns: "You are in danger of losing the chief executive of the association."
Mr Stewart says he attempted to pursue a motion of no confidence in Mr Satti earlier this year but was persuaded to withdraw it after receiving assurances that Mr Satti would "behave himself".
He had accused the company secretary, who is from East Dunbartonshire and chairs the children's panel there, of breaching confidentiality, lacking trust in other directors, arranging private meetings of selected directors and incurring unnecessary expenses.
Most seriously Mr Stewart accuses Mr Satti of "inappropriate behaviour towards a member of staff causing her to issue a complaint against directors of the company because of the stress incurred due to his action".
This is understood to be a reference to Mrs Hill, who has been on sick leave for some weeks.
Mr Stewart continued: "Although these matters have all been discussed at several executive board meetings, I do not believe that any improvement has taken place."
He claims he was effectively frozen out by other directors after his move against Mr Satti, receiving no information on items discussed by the office-bearers or any e-mails circulated to the executive since January.
There was "a complete disregard" for the opinions of other directors, Mr Stewart says, and a "lack of coherent minutes and reports" because staff had been excluded from meetings.
Alan Smith, the SSBA president, would not be drawn on Mr Stewart's allegations but added: "Negotiations between Mrs Hill and the executive are at a delicate stage. Outside influences are therefore unwelcome at this point."
Mrs Hill was unavailable for comment. Mr Satti could not be contacted.
Hints, rumours and innuendoes
In a letter circulated to all executive members, Ann Hill said that she faced "a fundamental breakdown in the relationship of trust and confidence" with the executive.
She accuses unnamed board members of "continual harassment, constant undermining of my authority and status, repeated questioning of my administrative ability and honesty, disclosure of my medical history beyond the confidence of my line manager, as well as hints, rumours and innuendoes".