The two heads' associations say the guidance will force members to keep disruptive pupils in school who they would normally have expelled to protect the interests of other pupils and staff.
Social Inclusion: Pupil Support says headteachers should only exclude children for serious breaches of rules after alternative strategies have failed, and where the pupil's continued presence would "seriously harm the education or welfare of other pupils or staff".
If heads fail to follow the guidance, governor discipline committees and independent appeal panels should reinstate pupils, it adds. Education Secretary David Blunkett will also frown on exclusions for first-time offences.
John Dunford, general secretary of the Secondary Heads' Association, said: "While we support the Government's social inclusion agenda, we are very concerned this guidance will make it much more difficult for schools and headteachers to maintain good behaviour.
"We see this guidance as weighted against schools. It's our decreasing ability to safeguard other pupils, and teachers, which is of enormous concern to us."
David Hart, general secretary of the National Association of Head Teachers, said most schools had pastoral systems for pupils at risk of exclusion. The problem was the declining level of support from education authorities.
He added: "I would strongly oppose any attempt to require governing bodies to overturn heads' judgments, when those decisions may be perfectly correct and proper. Heads run schools. Guidance is to help and not to control."
The guidance covers education authorities, and suggests councils should set up reintegration panels to look at services for excluded pupils - with the aim of getting them back into school.
From September 2002, education authorities will have to provide full-time education for permanently excluded pupils. At present, most offer a few hours tuition a week.
Copies of Social Inclusion: Pupil Support are available from the DFEE telephone 0171 925 5637.