Imagine a deadly disease so infectious that you could catch it from a colleague, a friend, a fellow bus passenger. A killer that no one fully understands, with no known cure, spreading like flu. A modern-day Black Death.

This is one of the scenarios we are told we must prepare for - not by scaremongers, but by a committee of scientists, medical experts and ethicists appointed by the government to consider how to regulate transplants of organs and tissues from animals to humans. Aids is thought to have come from monkeys, new-variant CJD from cows. Who knows what could happen when we transplant hearts from pigs or livers from baboons?

Xenotransplantation - as the practice is known - has a long and grotesque history, since the first transplant of a pig kidney into a human in 1906. Other experiments have included kidneys transplanted from goats, sheep and chimpanzees, livers and bone marrow from baboons, hearts and skin from pigs. In California in 1982, a baby lived for three weeks after being given a baboon's heart. But most of these experiments have been one-offs, often done by mavericks, sometimes illegally (a doctor in India is in jail for transplanting a pig's heart into a human).

In the past few years, however, the science has made staggering advances, and medical companies are pushing hard to conduct large-scale trials. As of next year, Britain will probably witness its first animal-to-human transplants: "source animals" have already been genetically engineered and bred in sterile facilities to keep them germ-free; medical objections have been largely overcome; biotech companies have invested and lobbied; and the government has drafted regulatory guidelines.

The UK Xenotransplantation Interim Regulatory Authority (UKXIRA), the committee of experts in charge of giving the go-ahead, will finalise those guidelines next month. In the meantime, it will consider an application lodged last month to conduct Britain's first full-scale trials to assess the effects of transplanting bits of animals into living human patients.

One claim made about xenotransplantation is that it could save the lives of thousands of people; another is that it could lead to a lethal epidemic. Yet despite being one of the most far-reaching developments in medicine today, it has failed to appear in our media - beyond a few scare-stories. The government and the biotech companies are doing their best to keep the public in the dark, and debate at bay. In the wake of the GM food debacle, they know the wrath of public opinion when scientists start dabbling in the very stuff of life.

Government guidelines - on the breeding conditions for the animals, how patients must not have children, and how to contain any outbreaks of dangerous infectious diseases - have been drawn up for consultation. Yet the Department of Health issued no press release about them, and was careful to send the guidelines out only to a few carefully selected individuals.

Imutran, the Cambridge-based company that pioneered the genetically "humanised" pigs - engineered so their organs aren't instantly rejected by the human immune system - insists it can't possibly confirm that it is breeding such transgenic animals in Britain. But Dr Corinne Savill, its chief operating officer, will in the same breath happily insist that the Home Office inspects its transgenic pig farm. Imutran does admit that it would like to start transplanting pigs' kidneys into humans within a year and a half.

When a company applied last month for permission to conduct the first xenotransplantation trials in Britain, there was no announcement - I only found out because I asked the right question at the right time. But the Department of Health spokeswoman insisted she couldn't possibly tell me the name of the company involved or the nature of the transplant. When I asked the reason for this secrecy, she pleaded "commercial confidentiality".

The "commercial confidentiality" statement is revealing, not just about the secretive nature of the British government, but about the motive behind xenotransplantation. Profit.

A recent study by the finance house Salomon Brothers reckoned that by 2010 the industry could be raking in profits of $6 billion a year. Research into xenotransplantation is all being done by huge drugs companies, most of them American, all with Buck Rogers names like Alexion, Genzyme, Nextran and Circe Biomedical.

John Dark, consultant heart surgeon at Freeman Hospital in Newcastle, and one of the members of UKXIRA, says the huge costs involved make it impossible for universities to afford to breed herds of transgenic pigs on sterile farms. Alix Fano, of the New York-based Campaign for Responsible Transplantation, insists that "Xenotransplantation is not about making sick people better. It's about making big corporations richer."

The potential for xenotransplantation is huge. There is strong evidence that it could find cures for otherwise incurable diseases. By slaughtering pregnant genetically modified sows, chopping out the foetuses, cutting off their heads, sucking out their brain cells and injecting them into the heads of humans, they may develop a cure for Parkinson's disease - at the moment, drugs can only suppress the symptoms until the inevitable occurs. A recent study in the US showed that similar treatment might also relieve the symptoms of stroke.

But the biggest impact of xenotransplantation is likely to be on tackling the acute shortage of human donor organs. Salomon Brothers reckons there's a demand for 250,000 kidney transplants a year worldwide. John Dark says the shortage of donor organs means that only 260 people in Britain get a heart transplant each year, but that there is an identified medical demand for at least 2,600. Multiply that by perhaps £50,000 for each transplant. And that's just Britain.

However, the dangers of xenotransplantation are also huge. Dr David Cook, a medical ethicist at Green College, Oxford, who also sits on UKXIRA, admits it can never give a 100 per cent guarantee that animal to human transplants will never lead to a dangerous infection. Hence, it is devising plans for incident response teams and emergency legislation to detain people in case of an infectious outbreak. Cook admits he can't rule out the need to call in the emergency services if things go really badly wrong, "but I don't envisage that scenario".

But in the absence of real debate, the drugs companies will have their way. One company doing xenotransplantation research published a study in August which purported to provide very strong evidence that transplanting bits of pig to humans doesn't lead to infection. Dark admits the study is persuasive, and that it is "fair to say" it has brought forward trials in the UK (and he is one of the people who will decide if the trial that has just been applied for can go ahead).

But it would be disastrous to let the drugs companies define the terms of the debate. US research has shown that, when the companies pay for tests on their products by "independent" scientists, the results are - surprise, surprise - more flattering than if someone else paid for them. There is no such thing as true objectivity, even in science. Hence the need for an open debate.

The government could find it has a furious backlash on its hands if it ducks the debate, and tries to spring xenotransplantation on a public kept in the dark. This time, it's not comparatively innocuous genetically modified maize we're talking about, but parts of specially bred, genetically modified pigs being transplanted into humans. It's a concept that fills most people with horror. The debate - when it finally comes - will be passionate.

The author is health editor of the "Observer"