During his flight to the US on Tuesday the Pope spoke of his own deep shame about the crisis, which has cost the US Church $2bn (£1bn) in compensation settlements.
He vowed to work against a recurrence, saying "we will absolutely exclude paedophiles from the sacred ministry".
Speaking to the US bishops at a national shrine in Washington on Wednesday evening, Pope Benedict asked: "What does it mean to speak of child protection when pornography and violence can be viewed in so many homes through media widely available today?"
"Responding to this situation has not been easy and, as the president of your episcopal conference has indicated, it was sometimes very badly handled," he said.
He was referring to earlier words by the president of the US Conference of Catholic Bishops, Francis Cardinal George of Chicago.
Cardinal George said the consequences of the scandal and its poor handling by the clerical hierarchy "makes both the personal faith of some Catholics and the public life of the church herself more problematic".
During the first Papal visit to the White House for almost 30 years, the German Pope urged Americans to use their faith to inspire "reasoned, responsible and respectful dialogue".
There were huge cheers as Benedict XVI and Mr Bush took the podium for the national anthems of the Holy See and the US, and a spontaneous version of Happy Birthday.
BBC Rome correspondent David Willey, who is travelling with the pontiff, said Pope Benedict studiously avoided any direct reference to the war in Iraq or to the current campaign to elect a successor to President Bush.
He did however, make an oblique reference to the tragic sacrifice of human lives caused by past conflicts and by implication, as a result of the current war in Iraq, our correspondent says.
The topic was discussed in the private talks, the White House said, with the leaders expressing concern about the plight of Iraq's Christian minority.
A joint statement said they both hoped for a "prompt and comprehensive solution to the crises" inflicting the Middle East.
Ground Zero prayers
One key issue the Pope said he would raise was immigration, as he feared the danger of family break-ups caused by mass migration of mainly Catholic people from Latin America.
15 Apr: Arrives at Andrews Air Force Base
16 Apr: White House luncheon; talks with Mr Bush. Meeting with US bishops and prayer service in Washington (evening)
17 Apr: Washington Mass; addresses Catholic University; interfaith meeting
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