John Wilson was speaking after information about pupil attacks on teachers was obtained by the Sunday Times Scotland and then followed up by other journalists.
Mr Wilson commented: "Two of our schools have been very adversely affected by these reports which were subsequently reported in other national media, often without comment on the context in which they were recorded.
"Auchenback primary school in Barrhead, an excellent school in every way, has had morale damaged by reports that it qualified as having the second highest level in Scotland of pupil attacks on teachers, and Neilston primary school, again an excellent school, was listed as one of the 10 most violent schools in Scotland.
"The fact is that the statistics reflect our policy of recording every physical contact with teachers, whether violent or otherwise, for pupils with additional support needs. Such recorded contacts make up the vast majority of the so-called assaults recorded. Neither school can be classed as 'violent' by any stretch of the imagination."
Mr Wilson also commented on reports that one pupil attacked teachers 35 times in one year, which he said was "technically true". But the incidents took place in 2003-04 when the pupil was aged six; he was later diagnosed as suffering from a variety of behavioural disorders. Following intervention, there have been no further incidents.
"The picture of a tiny terror machine, painted by some of the headlines, is simply not true and shows just how misleading figures that we are forced to reveal without contextual comment under FOI can be," Mr Wilson said.
Mr Wilson then refuted reports that East Renfrewshire had to start "self-defence" classes for teachers. "That is untrue," he said. "We do run courses on legal and safe restraint within the context of the needs of some pupils with additional support needs. These courses are a million miles away from self-defence."
Mary Montague, East Renfrewshire's education convener and herself a teacher, commented: "The education of young people with additional support needs, whether in mainstream or special schools, is delicate and calls for sensitive handling and there is nothing to be gained by reporting statistics out of context."