Health authorities have warned the Department of Health that they believe some of the 250 separated children seeking asylum who have disappeared from their care over the last four years are being sexually or financially exploited.
In private correspondence with the department, the Health Service Executive (HSE) said it has taken several children back into care after their rescue from "desperate situations" by gardaí.
The chief executive of the HSE (East Coast Area), where the majority of children are placed, has also accused the department of failing to respond to repeated requests for additional resources to provide acceptable standards of care since 2001.
Lack of funding also means social workers are not able to follow up on all cases of separated children who are reunified with their families, or people claiming to be their families, according to the HSE.
Reviews of services for separated children by the executive in the east coast area and the south both highlighted a range of concerns over inappropriate standards of care for the hundreds of children in care.
The reviews and correspondence, released to The Irish Times under the Freedom of Information Act, show that health authorities believe all separated children have been either trafficked or smuggled into the country.
Some girls have been brought here for arranged, underage marriages, while others are believed to have been trafficked for prostitution, according to a review of services by HSE in the east coast.
The vast majority of separated children are placed in hostels, while others are placed in residential care, foster care or unsupported lodgings.
Around half of those who arrived here are reunited with family members, while the remainder end up in the care of health authorities. Some 174 such children were admitted into State care last year, and 225 in 2003.
In a letter to the Department in March of this year, the HSE warned: "The executive has on several occasions taken children into care following their rescue from desperate situations by the GNIB [Garda National Immigration Bureau]. It also a matter of fact that the vast majority of children coming into care have been trafficked into the country..."
While there have been developments in the service - such as new facilities for 12 to 16 year olds - the executive has been unhappy with the standard of care and the levels of funding available to it.
It says it has been forced to take staff from other parts of the service to provide at least "a minimum standard of care". However, in the main, funding requests to the department since 2001 "remained unanswered despite repeated submissions".
In response, the department said in April this year that additional funds were not available for the service. It also raised concern that the executive was of the view that services could not be enhanced within existing resources, in light of the declining numbers of unaccompanied minors.
Responding to the reports, Dr Pauline Conroy, author of two reports on separated children and trafficking, said it was disturbing the Government did "not appear to have grasped the gravity of the situation".
"There are serious child protection issues here. There are vulnerable children from outside the EU. We have an absolute obligation to ensure they do not fall into the hands of predatory adults, whether that's employment or the sex industry."