The joint inspection report, published today, paints a picture of ineffective planning, delayed reports, quick turnover of social work staff, problems with information- sharing, poor feedback, and variable practice in record-keeping.
Inspectors reported they were "not confident that all children who had come to the attention of services needing help to keep them safe from abuse and neglect had been properly assessed and protected".
Younger children, who were identified as being at serious risk of harm, often received the help and support they needed, particularly if there were significant concerns about parental substance misuse.
But, the report found that older children did not and, as a result, were left "in high risk situations or without adequate support".
Although inspectors recognised that services were improving, following the independent report in 2003 into the killing of 11-week-old Caleb Ness by his father, they nevertheless signalled that "much more" needed to be done.
The report comes weeks after Edinburgh City Council's children and families department admitted it was facing an overspend of pound;14 million. More than pound;7 million went on protecting vulnerable children.
The report found major weaknesses in responses to children's immediate concerns. The meeting of children's needs, including assessing the risks they faced, was said to be "weak", as was overall leadership and direction.
Only the vision, values and aims of the leaders of the council, NHS Lothian, and Lothian and Borders police were deemed "very good".
Other failings identified in the report were:
* No co-ordinated approach for vulnerable children who moved from one area of the city to another;
* Insufficient foster care and residential unit placements;
* No assessment of friends and relatives with whom some children were placed;
* Frequent changes of social work staff in a large number of cases;
* Some children on the child protection register did not have an allocated social worker or named professional.
Assistant Chief Constable Neil Richardson, chair of the child protection committee in Edinburgh, said a working group had been set up in response to the issues raised. He said the committee would aim to ensure staff had the support they needed to provide essential services.
Marilyne MacLaren, the city council's convener for education, children and families, said an additional pound;6 million had been allocated to meet the needs of vulnerable and at risk children since the new SNP-Liberal Demo-crat administration had taken over the council.