Both the Local Government Association (LGA) and Association of Directors of Children's Services (ADCS) have issued the warning in response to government proposals to abolish local safeguarding children boards (LSCBs) and replace them with a new system of multi-agency arrangements.
These would involve councils, police and health organisations as core partners but not schools, according to proposed changes to Working Together guidance designed to pave the way for the new arrangements.
"A failure of schools to engage in local arrangements would create a hole in the system that could fundamentally compromise its effectiveness," states the LGA's response.
"Further, we are disappointed that the provisions outlined in the guidance still place the onus on the three core safeguarding partners to attempt to engage schools, rather than placing a clear duty on schools to play their part as full partners in line with the expectations on local authorities, health and the police."
The ADCS has described the omission of schools as partners in the new arrangements as a "missed opportunity" as "education settings typically have the greatest levels of contact with children and young people as a universal service".
"Schools must be at the forefront of these efforts - by the time concerns come to the attention of the local authority (via a referral to children's social care), police (via a callout) or health partners (via presentation at the GP or A&E) significant harm may have already occurred," adds the ADCS's response.
The new arrangements would also replace serious case reviews with a new system of local and national reviews, with clinical commissioning groups and councils given joint responsibility for child death reviews.
The ADCS is worried that this could lead to the "over medicalisation" of the process and "could limit opportunities for genuine learning".
Under the new arrangements safeguarding partners are also allowed to choose which "relevant agencies" should be part of new safeguarding arrangements.
But both the ADCS and LGA are concerned that regional schools commissioners, who oversee academies and free schools, are not listed among this group.
"It would be helpful if regional schools commissioners were listed as they too have a role in safeguarding children and young people," states the ADCS's consultation response.
Earlier this month the British Association of Social Workers also criticised the reforms, labeling them "regressive and negative".
BASW is concerned that cash-strapped local services may struggle to fund the new arrangements, which it says are untested and not backed by evidence that children will benefit.
The ADCS shares further concerns raised by BASW around a change to the statutory guidance that would see social workers no longer having to consult managers on assessment decisions.
"This is a fairly significant amendment and ADCS believes this warrants further discussion about the drivers for this change and the potential implications this may have," adds its consultation response.