Vulnerable pupils are falling "under the radar" in schools that are missing or responding inappropriately to their needs, despite Government reforms following the Victoria Climbie tragedy.
Charities giving evidence to a Parliamentary committee told MPs that teachers need more training to spot and help children at risk, and that too often these children are being punished instead of helped.
Social workers and other children's services professionals need to work more closely with schools in a multi-agency approach, they said.
Jo Aldridge, director of the Young Carers Research Group at Loughborough University, told the committee that the education welfare officers who traditionally spotted such problems now seemed to have a much bigger caseload. "So who deals with the welfare of the children?" she asked.
Kathy Evans, policy director at the Children's Society, said schools were failing to identify the needs of vulnerable pupils, such as runaways, even when they had daily contact with them.
"They are going to school, but their needs as children are being kept under the radar," she said. "They aren't being spotted as being in some kind of trouble or at risk."
Ms Evans said that schools were compounding problems by disciplining pupils for bad behaviour rather than investigating what lay behind it. "There are children for whom school is an uncomfortable place," she said. "They get excluded and passed from school to school, and their behaviour is seen as a concern about, rather than for, them."
Research published by the National Foundation for Educational Research last month found that most children's services departments have had more impact on the internal working of councils than the children they are meant to help.
They found that only 27 per cent of secondary and 41 per cent of primary heads rated their school's accessibility to social services support as excellent or good.
Meanwhile, an ICM poll showed that 56 per cent of heads thought it was "unacceptable" for schools to have more of a social services role.
The same proportion said that social services did not communicate well with their school.
Dr Aldridge said: "A lot of teachers do not see social services as their role, or they feel uncomfortable in a situation in which they have discovered a young carer at school, or found out that a pupil has a single parent with a serious mental health problem or who is terminally ill." She called for more training for teachers.