The Association of School and College Leaders (ASCL) predicts that if the trend continues, there will be a "significant increase" in permanent exclusions as schools struggle to cope with a lack of support and resources.
A poll of members showed that the number of exclusions of more than five days has decreased by 15 per cent since the new rule was introduced in September.
Headteachers also expressed concerns about access to the Child and Adolescent Mental Health Services, which can help schools avoid having to exclude pupils.
More than 80 per cent of the 50 respondents said it took more than a month to get a referral, and 42 per cent said it took more than three.
Nearly all said more effective support on emotional and behavioural issues would help reduce exclusions.
John Dunford, general secretary, will also be raising the concerns of school bursars who have suffered pay cuts as a result of the single-status agreement.
Under the agreement, local authorities have adjusted the salaries of some employees, to make sure workers are being paid the same for the same kind of work.
But the association has written to all children's services directors, calling for them to explain why some bursars have seen their salaries reduced by up to pound;6,000.
Dr Dunford said: "The role of the bursar is now in the senior management team, it is not simply an administrative role as some authorities have assessed it."