Declaring that "life must always be protected", a senior Vatican cleric has defended the Catholic Church's decision to excommunicate the mother and doctors of a nine-year-old rape victim who had a life-saving abortion in Brazil.

Cardinal Giovanni Batista Re, who heads the Pontifical Commission for Latin America, told reporters that although the girl fell pregnant after apparently being abused by her stepfather, her twins had, "the right to live, and could not be eliminated".

In an interview with the Italian newspaper, La Stampa, the cardinal added: "It is a sad case but the real problem is that the twins conceived were two innocent persons. Life must always be protected."

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Police believe the girl was sexually assaulted for years by her stepfather, possibly since she was six. That she was four months pregnant with twins emerged only after she was taken to hospital complaining of severe stomach pains.

The controversy represents a PR nightmare for the Vatican. The unnamed girl's mother and doctors were excommunicated for agreeing to Wednesday's emergency abortion yet the Church has not taken formal steps against the stepfather, who is in custody. Jose Cardoso Sobrinho, the conservative regional archbishop for Pernambuco where the girl was rushed to hospital, has said that the man would not be thrown out of the Church, because although he had allegedly committed "a heinous crime", the Church took the view that "the abortion, the elimination of an innocent life, was more serious".

The case has set off fierce debate in Brazil, where abortion is permitted only in cases of rape or a medical emergency. Brazil is one of the most populous Catholic countries, but conservative attitudes in rural areas are strongly at odds with the relatively progressive public view of abortion in major cities.

Even the President, Luiz Ignacio Lula da Silva, has waded into the row. "As a Christian and a Catholic, I deeply regret that a bishop of the Catholic Church has such a conservative attitude," he said "The doctors did what had to be done: save the life of a girl of nine years old. In this case, the medical profession was more right than the Church."

One of the doctors involved in the abortion, Rivaldo Albuquerque, has raised the prospect of public clashes at his local church, telling Globo, the nation's main TV network, that he would keep going to mass there, regardless of the archbishop's order. The young girl at the centre of the case escaped excommunication only because she is still a child in the eyes of Church authorities. The stepfather, who is 23, was arrested last week, apparently trying to escape to another region of the country. Police say he is also suspected of abusing the girl's handicapped 14-year-old sister. He is in protective custody, and if convicted faces up to 15 years in prison.