The Ombudsman for Children is investigating a substantial number of cases of children being physically assaulted or verbally abused by adults in schools and hospitals.
Speaking at the launch of her office's annual report, Emily Logan said she was worried that such children did not have a voice and that public bodies did not always act in their best interests.
"Some of these cases involve children being hit, physically abused or verbally abused. Yet public bodies are dealing with these cases in different ways, sometimes through the child protection route or else through the disciplining of employees," she said.
"There needs to be a national code of practice that develops better co-operation between public bodies to make sure that children's safety is protected," she added.
The Ombudsman for Children accused the State of falling short of its duty in supporting and protecting vulnerable children and families with extra needs, after demand for her office's services rose 43 per cent last year.
Ms Logan said 741 complaints were made to the office in 2007, compared to 517 during 2006.
Education was the main source of complaints (44 per cent) and related to issues such as support for children with special needs, procedures, policies and school transport.
"Seventy-five per cent of complaints came from family and extended family members, all of whom express frustration at the difficulty they have accessing adequate services for their children," Ms Logan said.
"In some cases families are dealing with a wide range of state agencies and complicated application processes while trying, as primary carers, to ensure basic services for their children. It is unacceptable that this additional burden is placed on already stressed families who find themselves in vulnerable situations."
More than 300 complaints were made about education, with the majority of complaints made about the Department of Education rather than individual schools, and were regarding special needs allocation, school transport, the handling of bullying, mechanisms for handling of inappropriate behaviour towards children, and procedures and policies.
The health sector generated 28 per cent of complaints, with most complaints were regarding the provision of HSE services such as speech and language and occupational therapy, child protection and decisions regarding children in care.
Youth justice, which relates to the treatment of children in detention, accounted for some 8 per cent of complaints.
For the first time the Children's Ombudsman heard from young people in detention about the nature and type of their placements. A key area of concern for Ms Logan was the lack of independent assessment of residential care services for children with disabilities.
She said social services inspectors do not have any remit at present to inspect residential care services for children with disabilities. Ms Logan said she was told by health authorities that independent inspections may not begin until 2009.
On the issue of mosquito devices - an ultrasonic youth deterrent - Ms Logan said she had written to the Minister for Justice to express concern about the possible use of such devices.
She also said the Garda Commissioner had told her that all rank-and-file members have been directed to fully investigate any complaints received with a view to seeking the directions of the Director of Public Prosecutions.