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"We could be drifting towards something to the detriment of our young people; something that will be deeply regretted in future," Mr McIvor, said in a message on the school’s official Facebook page.
Mr McIvor acknowledged a range of views for and against legalisation in the lead-up to the referendum, but said he was "struggling to see how legalisation would improve the lives of young people in New Zealand".
" I fear that it would make them worse," he said in his Friday evening message.
Several of more than 130 people who responded to his comments supported his views, and one person said it had taken "a lot of courage" to speak out, and this was appropriate from a school principal.
However, many people took issue with his comments and several strongly questioned the appropriateness of using the school’s official Facebook site to give a personal view.
One concerned person drew the matter to the attention of the Otago Daily Times, also on Friday evening.
That person queried whether "a statement that was against the legalisation of weed" should be allowed on the school’s official internet page, given restrictions on state agencies promoting political views.
The Ministry of Education’s internet site points out that party political advertising, including billboards, cannot be allowed in school grounds and that "as a state agency, you need to be politically neutral and can’t encourage electors to vote or not vote for specific parties, policies or candidates".
Another person said that a complaint would be lodged with the "appropriate authorities" over the matter.
Early this afternoon, King’s Board of Trustees chairman Richard Wingham issued a statement on the Facebook page, to "clarify" the position, in response to "feedback on the post by our Rector", and said he had expressed a view as the Rector, based on his "extensive educational experience".
Mr McIvor had not suggested to readers how they ought to vote on the issue, "nor did you intend to do so", Mr Wingham said.
"The Board of Trustees confirms it holds a neutral position in respect of the current cannabis referendum before Parliament.
"The original Facebook post has been left up on the basis that discussion in this area is seen as of benefit for the community as long as those comments are constructive," Mr Wingham said.
In his comments Mr McIvor asked if legalisation would " help their learning, growth and achievement or not?"
The proposed Bill had been promoted as "controlling" the availability of cannabis in our communities, and in our households.
But it was more likely to increase consumption , and to put "more cannabis directly into the lives of our young people, at a critical and sometimes vulnerable time in their lives".
The harmful physical and psychological effects of cannabis were well documented medically, and its dangers were "real and relevant", and had recently been highlighted, on behalf of the New Zealand Medical Association.
During his 26 years in secondary education, while working as a teacher, coach, dean, and senior manager,he had worked with pupils who were cannabis users.
"Often we saw apathy, underachievement and reduction in academic performance," he said.
Mr McIvor was not available for further comment this afternoon.