Professor Aynsley-Green called on strategic health authorities, acute trusts and primary care trusts that do not have a senior manager to preside over children's care to appoint one.
He said: 'The national service framework (NSF) for children and young people made sure we had these people in place - but with reorganisation, some of the posts have been lost. Who is in charge of children's services locally? They are not, as [Sir Ian] Kennedy pointed out in his report following the deaths of children who underwent heart surgery at Bristol Royal Infirmary, simply mini-adults in need of smaller beds and smaller portions of food.'
Professor Aynsley-Green said people in such children's posts should 'firstly understand children's services'. 'They must work with public health to understand the population they are providing healthcare for,' he said.
'They must know what they are doing now - when I have visited some trusts they could not tell me what they were spending on children's services, what they were providing or what workforce they had.
'Lastly, they have to talk to children and young people and listen to what they are saying.'
The commission's report said only 4 per cent of trusts scored 'excellent', 21 per cent 'good', 70 per cent were deemed 'fair' and the remainder 'weak'. It found that in 8 per cent of trusts, surgeons did not work enough with children to maintain their skills. In 12 per cent of hospitals there was not enough cover in the day to ensure effective paediatric support in an emergency; at night this rose to 18 per cent. Child protection remains a major risk: in 58 per cent of services used by children, nurses did not meet the required training standard.
Professor Aynsley-Green said: 'Not having cover to ensure emergency care for children needs to be recognised as a serious risk.'
The report also said that the value of play and communication must be given a much higher priority as only 24 per cent of nurses and 7-9 per cent of surgeons and anaesthetists were formally trained in this area.
It also calls for networks to be set up to ensure that staff have enough experience with children. It suggests planned surgery services could be supported by a clinical network of local and regional providers of children's surgery. Key features would include an agreement about the roles of local and regional trusts for each surgical specialty; extensive outreach by regional trusts, where specialist consultants work in local trusts; and giving local staff the chance to work in specialist regional trusts.
Similar systems are recommended for emergency care and pain management.
The children's commissioner said: 'I support the networks but they have to be managed properly. Consideration has to be given to things such as transport links - the cost of petrol for poorer families and the lack of public transport for those in more rural areas.'
He also lamented the lack of funding and targets for the NSF and said there was a worrying view emerging that the NSF was not important.