The two sisters, along with four priests, are at the centre of fresh allegations of the abuse of minors in the diocese of Regensburg in southern Germany.
The new investigation was announced by a spokesman for the diocese, although there were no further details of when and where the abuse took place or how many children were involved.
The diocese is acting on some of the 300 claims of sexual or physical abuse at institutions run by the Church which have flooded in since Germany was swept up in a scandal which has also caused shock and anger in Ireland, the Netherlands, Switzerland, Austria and Brazil.
"The work of the last 14 days has shown us that serious wrongdoing was committed by spiritual leaders and members of the church," said the spokesman, Clemens Neck.
"We deeply regret what the spiritual leaders and church members did to these children and youths, and we ask for forgiveness on their behalf."
He said most of allegations dated back to the 1970s and had therefore expired under Germany's statute of limitations, but they would still be referred to the public prosecutors' office.
They concern the Etterzhausen school just outside Regensburg – a feeder school for the Domspatzen boys choir, which was led from 1964 to 1994 by the Pope's older brother, Georg Ratzinger, 86.
He has admitted that on occasion he slapped pupils in order to discipline them, but was not aware of any sexual abuse.
A leading Vatican expert, who observed the Catholic Church in the United States as it become embroiled in sex abuse scandals from 2002 onwards, warned that the scandal in Europe will only worsen.
"Based on our experience in the US, the Catholic Church will have to be ready for victims of abuse to be coming forward in growing numbers over roughly the next three years," Rev. Thomas Reese, a senior fellow at Georgetown University and the author of 'Inside the Vatican', told The Daily Telegraph.
"Every time there is a new story of abuse, it empowers victims and encourages them to stand up and say 'this happened to me too'.
"I think in Europe over the next few years you are going to see hundreds, if not thousands, of victims coming forward every week."
Italy's prime minister, Silvio Berlusconi, expressed his support for a letter the Pope issued to the Catholic Church in Ireland at the weekend in which the German-born pontiff expressed his "shame and remorse" for decades of "sinful and criminal acts".
It was an "extraordinarily effective response" to the sex abuse crisis, which Mr Berlusconi said was being used to discredit the Catholic Church by its enemies.
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