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The cocktail of students, drugs and alcohol can seriously impair a school's effectiveness and principals say they can't solve the problem on their own.
It's often hard for teachers to identify whether a student's problems are due to drugs or alcohol because they don't know what the kids get up to at weekends, principal Gail Armstrong says.
A new report from the Australian National Council on Drugs says schools need more support from governments and communities to tackle the problem.
The council surveyed more than 200 secondary school principals about difficulties for students and what drug and alcohol education is offered.
Alcohol and drug use were nominated as the third and fifth most difficult problems for schools to deal with - along with mental health and bullying both on- and offline.
There was a big disruptive impact from things that happened outside the school, like weekend partying.
Ms Armstrong, principal of Alexandra Hills State High School near Brisbane, said it was a hidden problem.
"A child might be particularly lethargic or unmotivated on Monday or looking as if they've got a bit of a headache," she told AAP.
"We don't know that that's because they've been partying or binge drinking on the weekend."
But it was a big concern.
"Instead of getting out and playing sport or relaxing or studying, they're either preparing for drinking or they're drinking or they're getting over it," Ms Armstrong said.
"It puts a big hole in their week in terms of the impact it would have on them if that's what they're doing."
A majority of principals told the ANCD if schools were expected to take more responsibility for addressing these issues then it was critical to have more trained personnel and funding available.
"Schools need a far greater level of support from governments, communities and the drug and alcohol sector," council chairman John Herron said.
The council says governments need to improve access to funding for intervention and education.
Existing programs should be reviewed to see how effective they are.
Parental attitudes, such as supplying alcohol for parties or turning a blind eye to drinking, also need addressing.