Zollitsch said he had briefed the pope about the situation in Germany, where more than 100 reports have emerged of abuse at Catholic institutions, including one linked to the prestigious Regensburg choir run by the pope's brother from 1964 to 1994.
"With great shock, keen interest and deep sadness, the Holy Father took note of what I had to say," Zollitsch told a news conference, adding they had not discussed the Regensburg choir or Georg Ratzinger, Benedict's older brother.
Zollitsch said he had informed the pope of the German church's plans for tackling the crisis, including the appointment of a special representative on abuse, and Benedict had encouraged the "decisive and courageous" adoption of the measures.
With the German church still collecting information about the total number of abuse cases, Zollitsch also said it was premature to talk about compensation for victims.
The German lay movement, We Are Church, criticised the meeting for not spelling out concrete measures to be taken.
"Instead of apologising to the victims from far-off Rome, Archbishop Zollitsch should go soon to meet victims, listen to them and seek ways and rituals of reconciliation with them," it said in a statement.
"It's unfortunate that Pope Benedict did not offer any words of sympathy for the victims or seek reconciliation with them."
It said the Vatican should "recognise sexual violence as a worldwide structural problem of the Catholic Church that increasingly obscures the message of Jesus".
It was also revealed on Friday that the pope had approved in 1980, while he was bishop of Munich and Freising, a priest accused of child sex abuse being given Church accommodation in his diocese for therapy.
"It was decided in 1980 to give H. [the priest] accommodation in a rectory so that he could receive therapy. The archbishop [now Pope Benedict XVI] took part in this decision," the German diocese of Munich and Freising said in a statement, confirming a report in the Sueddeutsche Zeitung daily newspaper.
But deviating from this decision, the priest, who the Sueddeutsche said was accused of abusing an 11-year-old boy in Essen in western Germany, was given spiritual duties in Munich.