The Ombudsman for Children has said "significant progress" has been made to improve services and supports for children with disabilities in the care of the State, but more work still needs to be done by State agencies.
Niall Muldoon said Tusla has been "extremely proactive" in addressing issues raised in the case of a teenager known as "Molly" two years ago.
However, he said there are still "substantial shortcomings" on the part of the Health Service Executive.
In January 2018, the Ombudsman published details of the case of Molly, a child with Down syndrome, who was placed in foster care.
The now 16-year-old also has severe autism and was placed in foster care after her birth.
Her foster family had contacted the Ombudsman to highlight issues over the provision of services and supports from State agencies.
A report carried out at the time by the Ombudsman found that "neither the HSE nor Tusla saw Molly as a child in care and also a child with a disability."
It said: "There was a lack of co-ordination which meant that services and supports provided by both organisations were insufficient."
The OCO also said it was informed by Tusla that "there were 471 other children like Molly, yet neither Tusla nor the HSE had a good enough system in place to ensure adequate supports were being provided."
In a follow-up review, which was published today, the Ombudsman said he was "pleased to see that Tusla, in particular, has been extremely proactive in addressing the issues raised by Molly's foster carers, and identifying other children who are in a similar position."
Mr Muldoon also said "there is no doubt" that both the HSE and Tusla are working much more closely at a local level for other children like Molly and their families.
"However, it is incomprehensible that two years on the HSE has still not managed to come to an agreement with Tusla to identify the children in state care nationally with moderate to profound disabilities," he added.
In a statement, the HSE said the report highlights that "more work is required to replicate and strengthen the efforts made in support of Molly across the state and in support of all children with a moderate to severe disability in this state."
It added that "the HSE and our colleagues in Tusla are absolutely committed to joint working under the protocol arrangement."
The HSE also said its service plan for 2020 "commits to provide high quality residential and respite care to persons with disabilities and their families, and which will include ring-fenced services to children with a disability, including those in foster care arrangements."
Tusla the Child and Family Agency said a lot of progress has been made in Molly's case in conjunction with the HSE, since the original report in 2018.
In a statement, the Chief Executive of Tusla said "there is a comprehensive care plan in place for Molly, and this is likely to lead to continued improvements in the joint working that is necessary in such cases".
Bernard Gloster also said the agency acknowledges that "there remains much work to be done and improvements to be made for children, who require both care and protection services on the one hand, and specialised disability services on the other".
The HSE and Tusla said they are both fully committed to working collaboratively under a joint protocol, which they have developed.
Disability groups have described the findings in the report as disappointing.
The Head of Policy at the Disability Federation of Ireland said it is "yet another example of the lack of co-ordination across public services for people with disabilities".
Joanne McCarthy said it was "very disappointing and disturbing to hear this case is still unresolved".
"Parents of young children with disabilities, right across Ireland, are struggling to deal with this lack of co-ordination on a daily basis," she added.
Inclusion Ireland's Community Engagement Lead said to see the children "falling between the cracks of two agencies, is extremely disappointing".
Mark O'Connor said "these are some of the most vulnerable children in the State, with moderate, severe and profound intellectual disabilities, who don't have a voice themselves".