The report found that schools and other public services were improving their work, but were still unable to safeguard the most vulnerable young people. Problems identified by inspectors included the use of unacceptable levels of force by staff to restrain pupils. Physical-control techniques had been used in some cases as punishment, when they should only be used to prevent injury, damage to property or a severe breakdown in order.
They also found that teachers were often unclear how to recognise signs of abuse or neglect, particularly when dealing with children with special needs.
They said the quality of child-protection systems and training in schools was variable. The Commission for Social Care Inspection visited all 555 state and independent boarding schools and found that 60 per cent did not meet all the national minimum standards for child protection.
Around 40 per cent of residential special schools also failed these targets. Other concerns included failures in information-sharing, especially in cases involving asylum-seeker pupils and those in foster care, and a lack of emphasis in personal, social and health education lessons on the harm children can receive from people they know. There was also too little re-checking of school staff's criminal records.
Inspectors said there was evidence that partnerships between education and other agencies were improving, but communication often remained poor between teachers and social workers.
This week, the children's minister, Beverley Hughes, said teachers would have to change the way they work if pupils' needs were to be met.
Addressing a conference organised by the Teacher Training Agency in London, Ms Hughes said: "This does not mean asking teachers to be social workers.
But they will need to focus on supporting and enabling pupils to learn as well as working closely with other professionals.
David Behan, chief inspector for social care, said: "Children are still being failed by the system."