A child with autism often has no sense of danger but, if they are attached to the dog via a link to the dog's jacket, they are more likely to be able to go on outings with their family.
The HSE said it carried out an examination of the programme and the many claimed benefits were largely unsubstantiated. There were concerns such as no objective research, no evidence of long-term effects, and no evidence that it improved "real life" skills.
Senior official Dr Cate Hartigan said the HSE, particularly in the HSE South region, has received requests and applications for funding to support the provision of dogs to assist children with autism or intellectual disabilities.
"Given the current economic climate the focus for the HSE is on protecting core activities such as residential, respite, day and core-therapy provision, as well as ensuring maximum cost efficiencies are achieved.
"Therefore, while the provision of assistance dogs for clients on the autistic spectrum can be a positive development, it is not presently a priority in the context of the development of autism services.
"It was also felt that the cost of providing this type of service was expensive when compared with the equivalent cost of a therapist that could provide intervention with proven benefit to children.
"The HSE South have a concern that a number of small services seem to be developing on an ad-hoc basis, most likely as a result of communities/ groups coming together to support individuals known to them, without an awareness of other groups operating in close proximity," she added.
Dr Hartigan, who was replying to a question from Fianna Fail leader Micheal Martin, said: "HSE South will be engaging with the Autism Assistance Dogs Ireland group to make them aware of the other groups operating in their area, so that opportunities for sharing scarce resources can be explored."