The annual report from the Ombudsman for Children shows the number of complaints lodged with the office is up more than 20% on the previous year.
In 2011, 1,393 complaints made to the ombudsman were new, representing a 22% increase, while 98 case were carried over from the previous year.
The report shows that the office dealt with 1,491 complaints in total last year, with the most common ones relating to the areas of health and education.
Complaints about issues in education represented almost half of all cases at 47%, up 9% on the previous year.
Issues included complaints regarding teachers or principals, as well as problems regarding school transport.
Health represented 37% of cases, down 5% on 2010, while complaints regarding justice issues represented 8% of cases - down 3%.
Parents continue to be the principal advocates for their children, submitting 76% of all complaints.
The report also shows that recommendations made in light of an investigation around a single child can promote systemic change for the welfare of all children.
However, Children’s Ombudsman Emily Logan said it was clear that respect for the views of the child was not being respected systematically in Ireland.
Ms Logan called on the Government to ensure there is fairness and equity in how resources are allocated and criticised public bodies for using the recession as an easy excuse for not providing proper services.
She told RTÉ’s Morning Ireland that public bodies are inclined to give a knee-jerk response to every complaint, saying that they are working with limited resources.
She said many of the cases that come to her office are not related to money.
“Our experience over the eight years prior to the recession, and it continues since the recession, is that in fact many of the cases that we look at relate to communicating with parents, inter-agency cooperation, sometimes territorialism, so it's not always about resources.”
“I'm concerned that people would very quickly, and in the first instance use resources as a reason not to provide a good service to children.”
Ms Logan also said that changes in personnel at the top of education, health and justice have resulted in a more co-operative response to her office over the past 12 months.
She said it would be better if public bodies developed stronger policies on engagement that were less reliant on the individuals concerned.
At the launch of the report, Ms Logan also said that the group who concerned her most are the young people who are still being detained at St Patricks Institution.
She said while 16-year-olds were no longer being sent there are up to 30 17-year-olds still being held at the institution.
A spokesperson for the Minister for Children described the current situation at St Patrick’s Institution as “unsatisfactory” but said that funding had been secured to redevelop the Children's Detention Centre at Oberstown to accommodate 17-year-olds.
She said the project is on track to ensure that no-one under 18 will be at St Patrick's Institution by April 2014.