Too many pupil councils are "greetin' meetings", Robin Harper, the Green MSP, and former guidance teacher, told the conference.
Schools had to be more adventurous and give pupil or student council budgets for their priorities. "If they don't have a budget to spend, all it does is show that democracy does not work," he said.
Mr Harper revealed that Scotland's first children's commissioner would be appointed shortly and would be expected to promote best practice on school councils and on anti-bullying strategies.
The commissioner would have to be aware of the rights of young people and review all the Parliament's policies and practices. "It is almost like a third chamber," he said.
Margaret Doran, head of schools in Stirling, said the commissioner should be truly independent and not be afraid to challenge the system on behalf of young people.
"A blatant example of this is to challenge the adult construct of antisocial behaviour orders for children as young as 12 years of age. The job will require someone who is courageous enough to challenge the mindset of adults, including politicians," MsDoran said.