Some teachers confuse serious emotional and behaviourial difficulties with naughtiness, according to Government-backed research.
The result is that some pupils' problems are not being properly identified - and may be made worse if teachers respond inappropriately.
The report, from Birmingham University, concludes with a plea for more money for staff development.
The commitment and approach of both teaching and support staff, and the effective leadership of headteachers, are key factors in creating the positive ethos seen in schools which successfully provide for EBD pupils, it says.
Effective headteachers in the 27 schools studied helped shape positive policies and staff attitudes towards EBD. One was reported to have cycled around his catchment area to ask shopkeepers about the behaviour of his pupils.
But the imposition of EBD-friendly policies from above tended to be resisted by classroom teachers. The best policies were developed and "owned" by all staff, including non-teaching personnel, says the report.
Professor Harry Daniels, one of the four-strong Birmingham team, emphasised the importance of a school's general ethos and values to developing good practice for EBD pupils. The actual values endorsed were less important than that they were widely supported and talked about.
"The schools where we found good practice were schools where people were concerned not only to talk about the values they believed in but to ensure those values decided their practice," he said.
"These attitudes were by no means identical for all schools. There were a variety of approaches but each school demonstrated a commitment to living out what they believed in and talking about what they believed in."
The team found that what works for mainstream pupils works for those with EBD. Good teaching, effective leadership, shared values and aspirations for pupils, appropriate curriculum, and an effective and consistently applied behaviour policy were all key characteristics of successfully inclusive mainstream schools.
But the research - based on visits to 27 primary and secondary schools in three education authorities - highlights problems with dealing with external organisations. Education, welfare, justice and health professionals rarely worked together, and communication and collaboration was not much better within and between education authorities and their schools.
"Many of the interviewed teachers were unaware of their education authority's policy on EBD," notes the report.
"Further there was no widespread, co-ordinated, multi-agency approach to meeting these pupils' needs either nationally or within education authorities. Collaboration and communication between agencies tended to be dependent upon personal contacts rather than formal arrangements."
Though some EBD pupils are unlikely ever to be catered for in mainstream schools, concludes the report, maximising inclusion is the most realistic goal for schools.
Copies of the full report - cost pound;4.95 - are available from DFEEPublications, tel 0845 6022260