Hospitals in Leicester, Leeds and the Royal Brompton in London are to stop performing heart surgery on children, it was announced on Wednesday.
In a move to streamline paediatric heart services, three of the 10 specialist units in England will stop performing such procedures on children.
The move comes after an NHS review which concluded that expertise was spread too thinly in the 10 sites and should be concentrated in fewer hospitals.
The Royal Brompton in Chelsea, west London, Leeds General Infirmary and Glenfield Hospital in Leicester will not stop providing surgery immediately as plans to implement the new streamlined service are still being developed.
It is understood that the hospitals will continue to provide the specialist procedures throughout 2013.
Once they stop providing surgery the units will still see patients for diagnosis, monitoring and non-surgical treatment.
The consultation process was launched by the Joint Committee of Primary Care Trusts (JCPCT) of England as part of a national review aimed at streamlining paediatric congenital cardiac surgery services (PCCS).
The Safe and Sustainable review followed the landmark inquiry into children's heart surgery at Bristol Royal Infirmary between 1990 and 1995, where up to 35 children and babies died as a result of poor care.
In the wake of the inquiry, it was recommended that paediatric cardiac units be set a target for the number of operations per year, and surgery be concentrated in a few specialist centres in order to ensure quality of care.
One of the hospitals angered by the decision is the Royal Brompton which was at the centre of a bitter legal dispute surrounding the consultation process.
The hospital, which is the largest specialist heart and lung centre in the UK and among the largest centres in Europe, argued that the consultation process was unlawful.
But the Trust lost the legal row in April after it fought all the way to the Court of Appeal.
The Royal Brompton said that the proposals could put its future in doubt, but judges ruled that the consultation process was fair.
A spokeswoman from the hospital said as a result of the decision, the Royal Brompton will also lose its children's intensive care unit.
Bob Bell, chief executive of the Royal Brompton & Harefield NHS Foundation Trust, said: "It is very difficult to know what to say at times like these.
"But it is even more difficult to try and understand how this committee could have come to such a decision.
"Over the past 18 months we have seen respiratory charities like the Cystic Fibrosis Trust and Asthma UK, independent clinicians from around the world, and many anxious parents, highlighting time and time again the damaging effects on specialist respiratory care for children if Royal Brompton's paediatric intensive care unit is closed.
"I will now discuss this decision with the Trust's Board and Governors' Council to determine our next steps. One thing is certain - I will not be asking them for the mandate to manage the destruction of a highly valued and respected children's unit."
The institutions which will now house the specialist surgery centres are: Evelina Hospital, which is part of Guy's and St Thomas' Hospital Trust, Great Ormond Street, both in London, Southampton General Hospital, Birmingham Children's Hospital, Bristol Royal Hospital for Children, the Freeman Hospital in Newcastle and Alder Hey Children's Hospital in Liverpool.
Mike Collier, Chairman of Leeds Teaching Hospitals NHS Trust, said: "This result flies in the face of logical health care planning and plain common sense.
"We genuinely believe that the decision will not deliver the stated aims of the Safe and Sustainable Paediatric Cardiac Services review.
"This decision seems almost perverse in light of the information which became available during the course of the consultation process. We are surprised that the very clear wishes of over 600,000 people from this region appear to have been disregarded.
"On geography and population density alone the case for Leeds remains as strong as ever. We will now carefully consider, with our supporters, what action to take as a result of this very disappointing decision."
The Children's Heart Surgery Fund said it would attempt appeal against the decision.
Charity director Sharon Cheng said: "Today was a rubber stamping exercise. The panel has listened to clinicians and doctors and ultimately decided doctors know best.
"Clinical logic has not been taken into consideration. They have ignored co-location. They have ignored patient choice.
"We will now appeal to the health minister as he assured us a decision would be made on clinical logic. This has not happened today."
But the Children's Heart Federation welcomed the decision.
Chief executive Anne Keatley-Clarke said: "The delays to planned improvements in children's heart services caused a great deal of uncertainty for parents and professionals, so we are pleased for them that this has come to an end."
NHS Confederation chief executive Mike Farrar said: "This announcement will allow the NHS to get on with making long-overdue and necessary changes.
"We have had eleven years of debate on this issue. Now is the time to act and get children's care to highest standard possible."
John Radcliffe Hospital in Oxford was originally part of the consultation process but it suspended its children's heart programme in 2010 following a spate of deaths.
Dr Duncan Macrae, director of children's services at the Royal Brompton, added: "Anyone who has worked in the NHS for any length of time is familiar with reviews, reorganisations and reconfigurations.
"What is genuinely shocking about this proposal is the failure of NHS managers to acknowledge or understand the adverse impact that the proposed changes will have on our highly specialised services for children with severe lung and heart conditions.
"For instance, our leading children's lung disease service and its world class research programme will in my view be fatally wounded.
"How can this NHS reorganisation be an improvement, if services such as these are destroyed in the process?"
Bell added: "Royal Brompton has never argued for no change, just the right change.
"Safe and Sustainable should be about raising the bar of quality, protecting specialist skills and providing the best possible care, without question, for patients.
"But with this review, the steering group set criteria, and then ignored them when considering Royal Brompton's fate. Our service fulfills the set criteria, with four surgeons undertaking over 400 procedures each year.
"It is the third largest centre for children's heart surgery in the country, with very low mortality rates and an international reputation. Surely the NHS can do better than this?"
Sir Bruce Keogh, NHS medical director said: "These changes need to be made for the benefit of all children who have congenital heart disease.
"The review, which has been led by the NHS and is independent of ministers, has the support of the royal colleges as well as national charities.
"I hope that everyone involved can now work together to ensure the NHS delivers the very best services for children."
A spokeswoman from Great Ormond Street Hospital for Children NHS Foundation Trust said it welcomed today's decision "to concentrate children's cardiac surgery in fewer, larger centres and is delighted that the hospital has been one of the specialist centres selected to provide this service".
"We support the view that fewer, larger centres carrying out cardiac surgery will mean better outcomes for patients, with local centres continuing to provide follow up appointments close to the patients' home.
"The hospital will now work closely with other designated centres and hospitals affected by today's decision to ensure that there is a smooth transition for patients and their families to the new arrangements."
Dr Peter Carter, chief executive and general secretary of the Royal College of Nursing, said: "We know this has not been an easy process, however the NHS must continue to work to ensure better outcomes for children with congenital heart disease in the future.
"The Royal College of Nursing believes that concentrating surgical expertise and developing networks of expert cardiology care will give children born with complex heart conditions the best quality of care.
"On top of cardiac problems, many children have other complex conditions so it is vital to have experienced and highly trained teams of nurses and surgeons in these centres, ensuring better outcomes for children and young people. Children's cardiac specialist nurses working across the networks will enable children and families to receive as much care as possible closer to home.
"Now that today's decision has been made, we would urge its implementation as soon as possible."