During a 30-minute meeting with five abuse victims in Erfurt, Thuringia, the pope said he was "moved and deeply shaken by the sufferings of the victims," the Vatican said.
The, “highly emotional and very personal conversation deeply impressed the pope, as I believe, also the victims. The pope expressed his shame of what had been possible in the Church and that we must do all we can to resolve these crimes,” said Matthias Kopp, spokesman for the German Bishops Conference.
"The Holy Father expressed his deep compassion and regret over all that was done to them and their families," said a Vatican statement.
The meeting had been keenly awaited during the 84-year-old pontiff's visit to his homeland, which was rocked by revelations of widespread abuse over the last several decades.
"He assured the people present that those in positions of responsibility in the Church are seriously concerned to deal with all crimes of abuse and are committed to the promotion of effective measures for the protection of children and young people," the statement said.
"Pope Benedict XVI is close to the victims and he expresses the hope that the merciful God, Creator and Redeemer of all mankind, may heal the wounds of the victims and grant them inner peace."
Hans Langendörfer, the coordinator of the visit, told AFP the pope met three men and two women, who came from around the country.
It was very clear that the meeting had greatly touched the pope, added Langendörfer.
The leader of the world's 1.2 billion Roman Catholics had told reporters on Thursday on his flight to Germany that he sympathised with the thousands who had turned their backs on the Church over the paedophile scandals.
"I can understand that in the face of such reports, people, especially those close to victims, would say 'this isn't my Church anymore'," the pope said.
The German Catholic Church was thrown into turmoil last year as hundreds came forward saying they were abused as minors between the 1950s and the 1980s amid allegations that the crimes were swept under the carpet.
Over the past year large-scale paedophilia scandals have rocked the Catholic Church in a number of countries, including Ireland, Austria, Belgium and the United States.
During a visit to Britain this time last year, the pope also met five victims and expressed his "deep sorrow to the innocent victims of these unspeakable crimes."
The pontiff has previously met with victims on visits to Malta, the United States and Australia. In Malta the victims said the pope wept as he met them.
Late on Friday, the pope celebrated a sunset mass before 90,000 believers in a tiny village in former communist East Germany, which he praised for keeping the faith alive throughout the turmoil of the 20th century in Germany.
Christians in Germany are evenly divided between Catholics and Lutherans, with a growing trend toward secularisation sparking crises in both churches.
On Saturday, the third day of a tour of his native Germany, Benedict is due to greet the faithful in Erfurt's main cathedral square.
Later in the day, he will hold a prayer vigil in staunchly Catholic Freiburg in the southwest.