"One of the striking things about the system is just how isolated the teacher is in the classroom," Peter Peacock told the parliamentary education committee's inquiry into pupil motivation.
There was an increasing need to look beyond professional boundaries and share the best practices, especially in post-devolution Scotland, Mr Peacock argued.
He said the Scottish Executive had done more than ever before to encourage networking and other sharing initiatives. He believed there was an even bigger role to play in that area.
As Mr Peacock prepared to visit Finland again this week, he recalled from a previous trip there that one of the key features of its system was the way teachers shared practice as part of their professional craft and, as a result, performance had improved. "We must have the opportunity to do that," he said. "We need to bring teachers together within a school - that is hugely important."
He began his presentation to the committee by highlighting the broad indicators of motivation in the education system.
Teacher recruitment was up by 30 per cent; teachers were not rushing in droves to seek early retirement; marginally more children were staying on at school; more of the school population were taking exams; 5-14 attainment was improving; fewer students left without any qualification; and surveys showed that more pupils were satisfied with their school experience.
Mr Peacock also listed a number of negative indicators. An OECD study had shown that 27 per cent of pupils did not want to be in school and 56 per cent often felt bored. Thirty-one per cent said they were never given interesting homework.
A total of 21,000 pupils were excluded in Scotland last year. While that was only 3 per cent of the school population, it was nevertheless a significant number. The figures also showed that some 19 per cent of pupils truanted last year.
But the biggest issue was the fact that there had been no shift in the lowest attaining 20 per cent, equivalent to 12,000 pupils.
Mr Peacock said: "Overall there is a genuine, positive education system, pupils being reasonably well motivated. But it is clear there are problems at the bottom of the system. Internationally, we are also performing well, but not as well as some others."
The committee also heard from Bill Maxwell, HM chief inspector, who said that only a minority of schools faced serious discipline problems. Over the last three years, one in 12 secondary schools inspected had experienced broad, wide-ranging issues of ethos, discipline and behaviour. Much depended on the quality of leadership in a school.
A paper from the inspectorate also underlined the potential of integrated community schools to support disaffected and vulnerable youngsters. But it stated: "There is still some way to go to get good practice consistently embedded across Scotland in ways that might generate significantly improved outcomes for children."
Lord James Douglas-Hamilton, deputy convener of the committee and the Tories' education spokesman, asked if the system would be improved if headteachers, rather than the local authority, had the right to exclude disruptive pupils permanently from a school.
Dr Maxwell did not think it would be helpful if a pupil was left with nowhere to go. Authorities had to remain responsible for finding an alternative.
Learning and Teaching Scotland said in a paper for the committee that excessive assessment could be demotivating for pupils. "Pressures on schools from target-setting can transfer to pressure from teachers on students. The number of assessments makes learning less enjoyable."
The quality of teachers was the key factor in inspiring and motivating pupils, it suggested.