The Local Government Association said a £600m reduction in the education services grant (ESG) from central government, which covers the cost of such work, will mean many councils will no longer have the money to fund them.
Meanwhile, a change to regulations will mean councils can only undertake the duties if the school agrees to cover the cost from its own budget.
The LGA said the changes could affect a range of support services for schools, including criminal record checks on staff, safeguarding and mental health support.
It is claiming this will place more than five million pupils at risk "as schools are forced to decide what services they are able to maintain".
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