Pupils with social, emotional and behavioural difficulties can have a "halo effect" that upsets the behaviour balance of their classes, Richard Goring, South Lanarkshire, said. Several in the same class can make "teaching at best difficult and in some cases almost impossible".
Mr Goring, a depute head, said his experience in the past two years confirmed that a small number of pupils were referred repeatedly, almost period by period, because they were unable to cope in class.
"There are frequent interruptions to deal with disciplinary matters and continuity and interest are compromised," he said.
Confrontation was commonplace and threatening behaviour a daily feature.
"Those who know me, know me as an optimist but I find it difficult to be optimistic about the impact of a small number of pupils on the learning of the majority," he said.
Mr Goring pressed ministers to recognise the difficulties and introduce effective, fully resourced alternatives out of school.
Ann Ballinger, East Dunbartonshire, said that up to 80 per cent of pupils in her school told inspectors that they felt their learning was being damaged by one or two pupils in every class.
Delegates backed "zero tolerance" of violence against staff, supporting calls from Alan McKenzie, the union's president, for pushing, shoving and jostling to be included in official statistics.
But Bob McGarill, a Glasgow depute head, challenged colleagues who continually harped on about bad behaviour. "I do not believe discipline is disintegrating and schools are worse places than they were five, 10, 20 or 30 years ago," Mr McGarill said.
However, he appealed for maximum support and training for staff who had to take pupils who had been in special schools.
Classroom relations could be complex. In one bottom S3 maths group, five adults were in the room to take a class of fewer than 20, all with different jobs.