The guidelines were drawn up by the School Drug Safety Team chaired by Ken Corsar, director of education in Glasgow, following cases where pupils were caught in possession of drugs in schools.
A pack of support for schools launched at Hyndland Secondary in Glasgow last week by Sam Galbraith, Children and Education Minister, which will be sent to all schools, includes a 44-page guidance manual from the Corsar group, a small pocket guide and a parent's guide.
Mr Galbraith stressed the importance of every school having "an effective drug education programme that promotes healthy living".
The Executive now wants local inter-agency drug action teams to ensure that all schools in their area have written procedures for dealing with drug misuse in line with the School Drug Safety Team's recommendations.
Although the focus is on illegal drugs, the guidelines are also intended to cover abuse of solvents and alcohol.
An HMI report in March last year found that 60 per cent of primaries had no policy on drug incidents, although the figure for secondaries was only 15 per cent. Forty per cent of primaries - 87 out of te 222 surveyed - had no programmes to educate pupils about the dangers of drugs, a situation described by the then education minister as "unacceptable".
Among the list of dos and don'ts when interviewing pupils, the report suggests questions should be kept factual and the pupil's right to silence respected. There should be no assumptions about guilt and no body searches which could be considered an assault.
There is also guidance on how to handle inquiries by the media and schools are urged to demonstrate that "the incident has been taken seriously and managed effectively".
The report reinforces previous advice that local authorities should arrange for a "named person", either in the education department or elsewhere, to act as a point of contact for schools. Schools themselves should have at least one member of staff with basic training in recognising the signs of drug misuse, including the potential hazardous effects of drug-taking and how to respond to emergencies such as intoxication or overdose.
The drug safety team also underlines strongly the importance of every school becoming a health-promoting school. The aim is to ensure "not only that health education is integral to the curriculum but also that school ethos, policies, services and extracurricular activities foster mental, physical and social well-being and healthy development".