Addressing the latest Scottish Executive-backed ethos conference in Glasgow, Professor MacBeath added: "When it comes to the crunch and about more power being exercised by children, then everybody backs off. It is by looking at how to give pupils real responsibility and real power that we can actually improve our schools."
He called for a greater "culture of diversity" in schools and for pupils to enjoy more responsibility.
The current education Bill, which last week completed its passage through the Scottish Parliament, stresses pupil involvement in decision-making.
Professor MacBeath said a distinguishing feature of schools' cultures was the ability of the leadership to listen to different perspectives that sometimes conflicted with each other.
He also suggested teachers should control professional development, following the McCrone recommendations. "We have a view that professional development is something done to teachers, but if we really want teachers to develop professionally, then we have to put them in the driving seat of their own development.
"We should emphasise that professional development should be part of a professional vision, that this is something you do as a teacher and build that into what schools and teachers are about," he continued.
Meanwhile, Jenny Mosley, the pioneer in Britain of circle time, underlined the importance of listening to children's views.
"If children are given a chance to speak and be heard, this attitude makes them think their opinions are being valued. If opinions are valued and they have a voice, they feel empowered. If there is no forum for them to be heard, they will be disempowered and they in turn will disempower others. This is where bullying comes in," she said.
Dan McGinty, head of St Columba's High in Perth, winner of last year's ethos award, echoed recent calls for more resources to tackle social inclusion. As the volume of exclusions reduced and teachers were signed up t positive behaviour management, schools needed more support to deal with the small number of pupils causing difficulties.
"When we get to the level when small misdemeanours increase or there is a major incident and you are looking for a way to manage that within the school community, you really need resources. This could be people, or in our case, accommodation," he told a conference seminar.
The "culture of secrecy" is the biggest barrier to preventing all forms of in-school bullying - including staff bullying, Olwynne Clark, head of Clippens School in Linwood, said. It was only by disclosures that things improved.
Teachers were sometimes made to feel incompetent if they reported incidents, while school managements felt vulnerable when the climate was opposed to excluding pupils.
Veronica Rankin, equal opportunities officer at the Educational Institute of Scotland, reinforced the message that bullying of teachers by pupils, parents or colleagues had a de-skilling effect. Teachers began to question their own competence due to its persistent nature.
"Rather than admit it is the other person's behaviour that is unacceptable, teachers will often internalise it and begin to question why they are not dealing with this properly and why they are chosen for this behaviour.
"Neither should we forget the effect of institutionalised bullying. The more you ask teachers to do, with the systems that are in place, means that managements have to put increasing pressures on teachers," Ms Rankin warned.
Sam Galbraith, the Children and Education Minister, emphasised the importance of a good ethos for a successful school. It encouraged achievement and helped to celebrate success. "Children only get one chance at school and it is of critical importance that we do everything possible to ensure they get the best possible chance to achieve well," he said.
The conference saw the launch of The Ethos of Achievement, the latest publication to promote good practice across schools. The winner of this year's Schools' Ethos Award is Craigie High, Dundee. Runner-up is Pentland School in North Lanarkshire, a 14-pupil school for emotionally disturbed children.