The two-year project will target health services in 110 council areas where CQC research has shown children are at greatest risk.
It will take into account child protection concerns highlighted in latest inspection reports, serious case review findings and the length of time since services were last inspected.
The areas that are likely to come under scrutiny first include the 20 authorities that have been judged to be failing by Ofsted over the past few years, including Birmingham, Doncaster and Sandwell.
The health watchdog will also target areas based on whistle-blowing information from NHS staff.
GP surgeries, health visiting, school nurses, hospital emergency departments, maternity units and mental health are among the services to be examined. According to a CQC statement, “the focus is on the child’s journey through this maze”.
The inspections will also focus on how well local health services are working together to safeguard children. A lack of information sharing and communication across services that support children is a key factor highlighted in serious case reviews and in Professor Eileen Munro’s 2011 review of child protection.
Inspectors will also consider how “safe, effective, caring, well-led and responsive to children’s needs” services are, the CQC statement adds.
A particular focus will be on how health services are supporting children in care.
Inspectors will also look at the quality of child protection training and the timeliness of referrals to services such as mental health and substance abuse.
A specific issue the CQC will examine in hospitals and other acute care settings is whether they have alert systems in place to identify and track children who are at risk of harm.
This latest move by the CQC comes ahead of plans in 2015 for a multi-agency inspection of child protection across health, social care, education and the justice system that will involve Ofsted, CQC, HMI Probation, HMI Prisons and HMI Constabulary. Ofsted is to launch a consultation on the move next year.
CQC head of operational improvement Sue McMillan, said: “CQC and other inspectorates are working together to start a joint inspection programme in 2015. In the meantime, we are continuing to follow up our responsibilities in making sure children using health services are safeguarded from abuse and that children in the care of local authorities have their health needs met.”
The CQC previously inspected child protection jointly with Ofsted.
Rather than an Ofsted-style rating, CQC inspectors will make recommendations for improvement that will require a response from the service. There will also be a national report at the end of the first and second years of inspections.
NHS Confederation director of policy Dr Johnny Marshall said: "We have sadly seen some of the worst consequences of children and young people's services failing to join up around the individual. It is absolutely imperative that seamlessness between services improves, and this approach to inspection has the potential to shine light on gaps that have previously been harder to discern.
"One of the difficulties is that responsibility for commissioning children and young people's services sits with eight different types of organisation. Every transition point poses an additional risk to service users getting a smooth experience. It is really important that the CQC's new inspection programme considers not only each individual service but how well they knit together around the child or young person."
The announcement comes just a day after Ofsted unveiled its new single inspection framework for local authority children's social care services.
