Should Mr Hunt decide to give the treatment the green light the technique could be written into law as early as next year, making Britain the first country in the world to allow human trials.
Lisa Jardine, chair of the Human Fertilisation and Embryology Authority (HFEA), which is conducting the consultation, said the issue was of "enormous public interest", and not just to affected families.
She said: "We find ourselves in unchartered territory, balancing the desire to help families have healthy children with the possible impact on the children themselves and wider society."
Comparing the ethical debate with the birth of Louise Brown, the first IVF baby, in 1978, she added that many people had expected the child to be a "monster" and seen conception outside the womb as "absolutely appalling", but that IVF has since become commonplace.
She said: "Here, we are going that mile further which is a genetic modification of the egg. That is uncharted territory. I feel very strongly that once we have genetic modification we have to be damn sure that we are happy, because this is not about us.
"This is not about our children. It's not even about our grandchildren. It's about many generations down the line what the consequences might be."
An estimated one in 200 children born in Britain each year is thought to have some form of mitochondrial disease, with defects in anywhere between a handful and 90 per cent of their mitochondria.
In the vast majority of cases, where the number of defects is low, there are no symptoms and the condition is never even diagnosed.
But in about one in 6,500 people the level of damage causes the development of severe medical conditions including muscular dystrophy and ataxia, a neurological condition affecting balance, coordination and speech.
About 99.8 per cent of our DNA, including all our visible characteristics, is contained in the cell nucleus and is passed down from our father and mother in equal measure.
But a small fraction consisting of 37 genes is located in the mitochondria, the tiny structures which supply power to cells, and is inherited solely from the maternal side.
The new technique, being developed by researchers at Newcastle University, is designed to tackle a range of genetic conditions passed to children by their mothers through mutations in these genes.
The mutations can cause cells to malfunction or fail completely, resulting in complications which are especially severe in parts of the body which use the most energy - the brain, heart and muscles.
By removing the nucleus from a woman's egg before fertilisation and implanting it into a donor egg which has had the nucleus removed, and then using the egg in traditional IVF, doctors could cut damaged mitochondria out of the family line.
A similar technique could be used on an embryo by removing the nuclear DNA from the mother's egg and father's sperm and implanting them into a healthy donor embryo with its nuclear DNA removed.
The resulting child would inherit their identity from their mother and father, but they and all future generations would have the mitochondrial DNA of the donor.
A survey of 800 people by the Progress Educational Trust found that two thirds supported the use of the technique while a third opposed it, while a report by the Nuffield Council on Bioethics last year claimed the approach would be ethical.
The public consultation, being overseen by the Human Fertilisation and Embryology Authority, will run until December 7 with members of the public encouraged to register their views via a dedicated website.
There will also be two public events held in London and Manchester where people can learn about the technique and register their views. A report compiling the feedback will be published in March.
The panel appointed to oversee the consultation includes scientists as well as leading voices opposed to the treatment including Josephine Quintavalle, of the Comment on Reproductive Ethics campaign group.
She said: "This is not about curing disease in an existing human being, it is creating a new kind of embryo and the alterations you have made will pass on to future generations. You are playing around with the building blocks and restructuring how human life is created.
"Although IVF might be considered artificial it is just a way of repeating what happens biologically, but this is a considerable step in a completely different direction where you are changing those building blocks forever."
The Human Fertilisation and Embryology Act contains a window which would allow the current ban on techniques which alter inherited genetic material to be overturned by Parliament.
But the HFEA would have the final say on whether the treatment could be used in clinics, and it is likely that much more information on the safety and effectiveness of the technique would be needed before that was given.
Prof Mary Herbert, part of the team researching the technique at Newcastle University, said: "We want to make a difference to the lives of our patients who live with mitochondrial diseases.
"These can seriously affect the quality of life of both patients and their families and it often affects several generations. If we can stop that happening it will be a tremendous help for many hundreds of people who suffer with these diseases."
Dr Marita Pohlschmidt, of the Muscular Dystrophy Campaign, said: “For women who have been dealt the heavy blow of living with mitochondrial disease, the prospect of bearing healthy children is of immeasurable value.
"We believe that this technique could open up the possibility of motherhood untainted by the fear of passing on a painful, debilitating condition to their future children."
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