Every time Francesca lies down and has her ballooning stomach covered in gel for a routine scan, she looks at the strip light on the ceiling of her clinic in Sardinia and says a silent thank-you to a local female judge.

A few months ago, this 24-year-old mother from a village in the rugged Sardinian hills came close to a nervous breakdown. Two and a half months into a pregnancy, she discovered that one of the twins she was carrying had a genetic illness, thalassemia or "Mediterranean anaemia". But when she and her husband decided to remove the unhealthy embryo, they were told they would be committing a crime.

Under an Italian law on assisted reproduction passed earlier this year, their only options were to keep both children or abort them both. And abortion would only be legal if it was carried out within the following two weeks.

Francesca and her husband Luca's seven-year-old daughter was already living with thalassemia, common in Sardinia, and they knew what it meant. Fortnightly blood transfusions for life. Daily injections. Violent mood swings.

"It was a very hard decision," says Francesca, after a check-up with her gynaecologist, Dr Giovanni Monni, at the Ospedale Microcitemia in Cagliari. "For the child, and for us, living with thalassemia is like a prison sentence. I'll admit it, we just couldn't face doing it again."

But they had no intention of aborting both embryos. The couple were desperate. As the deadline for legal abortion approached, Luca stopped going to work. Francesca was sick with anxiety. They began making plans to have the foetus removed legally in London, when a local judge ruled against the state in their favour. The two-minute embryo reduction operation would not be a crime, the female judge said, as it was necessary to protect the mother's mental health.

The same judge ruled against the state in another case, that of a petite young woman from Palermo, barely four feet tall, who faced serious health risks if she gave birth to triplets; she, too, was able to remove one foetus. The woman had undergone IVF treatment and, under another clause of the disputed fertility law, doctors were obliged to implant three embryos at a time.

These two are among the few known cases of Italian couples who have won legal rulings that favour their personal circumstances over the rigid legislation passed by parliament in March, giving the embryo rights equal to that of a woman.

Dr Monni, a leading Italian fertility expert, is one of the few doctors who has taken practical steps to expose the contradictions and weaknesses inherent in the legislation. While he cannot risk his job by breaking the law, he has encouragedpatients to seek legal rulings that allow him to give them the treatment they need.

Under the existing law, forced through parliament to plug a 30-year legal vacuum, embryos have gone from being at the mercy of maverick doctors to having armour-plating. All forms of cloning and embryo research are now illegal. Only three embryos may be made in vitro at a time and all three must then be implanted at once. (There appears to be no clear scientific reasoning behind the three-embryo rule. Instead, it is a kind of political compromise, designed to balance the needs of older and younger women in a single rule.) Embryos may only be screened by the naked eye for genetic diseases or defects before implanting, and once implanted must be treated equally, regardless of abnormalities. Doctors face fines of up to €600,000 (£400,000) and a three-year suspension if they break the law.

The potential pitfalls were evident before the legislation was passed. The three-embryo rule increases the risk of multiple pregnancies for young women, and reduces the chances of women in their 40s becoming pregnant at all through IVF.

In the five months following the introduction of the law, the success rate for IVF treatments dropped from one in four to one in nine. But rather than turning to the courts, most of the estimated one-in-five couples who need science to help them conceive have simply given up trying, while others have headed abroad to escape the law.

Stefania Prestigiacomo, the minister for equal opportunities, has been one of the more vocal critics of the law from within the government. "Effectively, it discourages people from turning to fertility treatment to get pregnant," she says, speaking from her unglamorous Rome office where small children are occasionally found playing in the corridors. "There are some errors that need to be corrected. There is no doubt that some aspects of this law are against women."

Others put it more bluntly. "It's as if we are weirdos, social outcasts," says Federica Casadei, who runs a Rome-based support organisation for couples with fertility problems called Cercaunbimbo (Looking for a child). "If you are sterile, the state doesn't want you. And it doesn't help you. The embryo is so sacred now that you cannot touch it, not even to help it be born."

Cristina Zuppa, a younger mother whose attempts at in vitro fertilisation have so far failed, says: "This law is made by people who have no idea what it is like not to be able to have children. They are dictating to the nation on the most private of things. It's like being told what clothes you are allowed to wear."

Emma Bonino, the MEP and former EU humanitarian affairs commissioner, says that it is not that Italians have gone back in time with the new law, more that they have crossed the Tiber river and become "citizens of the Vatican". While Italians proudly cohabit with the Holy See and the vast majority are nominally Roman Catholic, when it comes to practical questions about family life, they tend to respectfully ignore the Pope. Some of the most valued legislative milestones in recent Italian history have been the legalisation of divorce (in 1970) and abortion (in 1978), wanted by the vast majority and opposed by the Vatican.

Over recent months, the fertility law has revived this tension. Roman Catholicism ceased to be the formal state religion in 1984, so who exactly makes the rules - the people or the Pope? It has also opened deep wounds for those who believe that Italy is run for men by men, be they politicians in limousines or priests in purple robes.

"I'm a Catholic and so are all my family," says Francesca at the Cagliari clinic. "But we believe you have to be realistic and do the right thing in some situations. Not what the Pope says. I think the men who make the laws [in Italy] don't have a clue what our reality is."

When the fertility law was voted through parliament, after 30 years of stalemate between traditional Catholic-thinking legislators and their opponents, the health minister Girolamo Sirchia said it was "a good start" towards protecting the embryo. "Research should be carried out on animals, not Christians," he said.

The law was passed by leftwing figures, too - their religious beliefs overriding any natural instinct to oppose Berlusconi's government. And although many were aware that there were weaknesses in the legislation, there was some collective relief in government that finally a law - however flawed - had been passed. Maverick doctors such as the controversial Severino Antinori could no longer claim to have cloned human beings, or help women over 60 conceive.

But the law met with outcry from scientists, including fertility expert Carlo Flamigni, and Rita Levi-Montalcini (who won the Nobel prize for medicine in 1986). The pair issued a joint statement, describing it as "astonishing from a scientific point of view and disgusting from a moral point of view".

Six months on, it looks as if the legal experiment has failed. Public opinion has been moved by the traumas the law has imposed on people like Francesca and Luca and there have been calls for the health minister, Girolamo Sirchia, to resign. Yesterday, campaigners announced that they had gathered more than one million signatures - double the 500,000 signatures required to call for a referendum on either modifying or abolishing the law. Two recent polls have shown that over half of respondents would vote to abolish the law.

The health minister has so far shown no sign of wanting to revise the more contested parts of the law. His office did not respond to repeated telephone and written requests for an interview.

"None of us were elected for our religious beliefs," says Prestigiacomo, the Catholic equal opportunities minister, who supports many but not all aspects of the law. "We do not have the right to impose our beliefs on others. Italy is supposed to be a secular state. It's a pity there is resistance [within government] to changing parts of the law. It means there is a real danger the public will vote to abolish it altogether and we'll be back to zero, where we were 30 years ago."

Now that a referendum seems likely to go ahead, it looks as though the government's attempt to regulate fertility treatment may have been one of the country's shortest-lived laws.

"It's an important day for women in Italy," campaigner Barbara Pollastrini of the Democrats of the Left said yesterday. "It is a yes to hope."