Children's neurosurgery is to be centralised at the University Hospital of Wales in Cardiff, meaning only an emergency service will stay in Swansea.
The University Hospital in Cardiff is the largest in Wales
Health Minister Jane Hutt has confirmed the recommendations of Health Commission Wales.
Health experts have claimed the plans were the best way to stop services being moved to England.
Plaid Cymru AM Dr Dai Lloyd said the announcement was a "bitter disappointment".
Neurosurgery treats disorders of the nervous system including diseases of the head, brain and spine.
The minister said her objectives were to provide "an integrated, audited, safe, high-quality, sustainable hospital and community-based multi-disciplinary paediatric neurosurgery service."
She said she wanted a service that "meets present and future needs, including current unmet needs, for the children and families of south Wales, and is provided by skilled accountable professionals as close to the child's home as possible."
She said her decision had been made, "with particular reference to the long-term therapy, care and support for the child with neurological damage".
But Dr Lloyd said: "It does ignore the huge furore that's in Swansea and south Wales west.
"It ignores the wishes of thousands and it ignores the decisions of Swansea Community Health Council and Neath Port Talbot Community Health Council, who are the patients' voices, after all."
The emergency service will be based at the neurosurgery unit at Morriston Hospital in Swansea.