The government is to push ahead with plans that would allow doctors to prevent major childhood diseases by creating IVF babies that have genetic material from three people.

The controversial procedure, called mitochondrial transfer, uses a snippet of DNA from a healthy female donor to prevent mothers passing on devastating genetic disorders such as muscular dystrophy and heart and liver conditions.

Pioneered in Britain by researchers at Newcastle University, the procedure targets diseases caused by faulty mitochondria – the tiny power units inside our cells. The disorders tend to affect parts of the body that need the most energy, including the heart, brain and muscles. Around one in 6,500 people is born with a mitochondrial disorder, making such conditions more common than childhood cancer.

Dame Sally Davies, the chief medical officer for England, announced the move at a briefing in London on Thursday. "It's only right that we look to introduce this life-saving treatment as soon as we can," she said.

A consultation by the Human Fertilisation and Embryology Authority (HFEA) published in March suggested the public was generally supportive of the technology. Draft regulations are expected to be ready this autumn.

If MPs approve the regulations, due to be debated in parliament next year, Britain would be the first country to endorse the radical treatment. Before the end of 2014 doctors would be able to apply for permission to offer the procedure on the NHS.

But some groups oppose the procedure because one approach involves the destruction of IVF embryos. The technique also crosses a line in medicine because it makes genetic modifications to an embryo that will pass down to all future generations. That raises the risk of unforeseen complications affecting generations to come.

While the procedure has been shown to work in animals, it has never been tested in humans. For this reason, Davies said any babies born through the process must be followed up to ensure they are healthy. "This is not a decision to take lightly," she said.

If approved, five to ten of the most severe cases could be treated in Britain each year. That number is likely to rise because faulty mitochondria are linked to an ever greater range of medical problems, such as diabetes, deafness, Parkinson's disease and even obesity.

Speaking at the briefing, Davies said mitochondrial disease can have a "devastating impact" on families. "People who have it live with debilitating illness, and women who are affected face passing it on to their children," she said.

Mitochondria contain only 37 genes, which are crucial to the energy supply of cells. The vast majority of our DNA, the 23,000 genes that shape our appearance and much more, is held separately inside the cell nucleus.

Scientists have developed two procedures to prevent faulty mitochondrial DNA being passed on to children. In both, genetic material from the parents is injected into a healthy donor egg with normal mitochondria that has had its nucleus removed. The resulting embryo carries DNA from its parents as usual, but its mitochondrial DNA – amounting to 0.2% of the total – comes from the donor.

Unlike sperm and egg donors, women who donate healthy mitochondria would almost certainly remain anonymous and not be traceable, Davies said.

Mitochondrial diseases are incurable and there is currently no way to prevent them being passed on. Specialist clinics already offer chorionic villus sampling (CVS) around 11 weeks into pregnancy, which can pick up genetic abnormalities. Other women have IVF with donor eggs, or choose instead to adopt.

Doug Turnbull, who leads the Newcastle team pioneering the procedure, said: "This is excellent news for families with mitochondrial disease. This will give women who carry these diseased genes more reproductive choice and the opportunity to have children free of mitochondrial disease."

But Helen Watt at the Christian Anscombe Bioethics Centre in Oxford condemned the procedure, claiming it involved the deliberate creation of an embryo "as a source of spare parts". She added: "Parenthood is about unconditional welcome of children. It is not about manufacture and control. Couples who do not want to take the risk of passing on mitochondrial disease might want to consider ethical alternatives like adoption, which are far preferable to pursuing dangerous techniques of genetic engineering which exploit both embryos and egg donors."

Sarah Norcross, director of the Progress Educational Trust, welcomed the government decision to pursue the new technique. "It would be unethical not to offer this treatment if it is safe and will help prevent children being born with serious disease. The other options are not great," she told the Guardian.

Robin Lovell-Badge, a geneticist at the National Institute for Medical Research in London, said experiments so far showed the procedure was safe, but there was always an element of risk when a new technique was tried in humans for the first time. "It will of course be a brave decision for the first families, and for the HFEA as the regulator, to decide to go ahead once the regulations are approved by parliament, but more often than not, progress requires some element of bravery."