Schools must "provide a safe environment" for children, Pope Benedict XVI said on the second day of his UK tour, as five people were arrested over a potential threat to the pontiff.
In an apparent reference to the abuse scandal, the Pope said teaching should be carried out in an atmosphere of "respectful and affectionate trust".
But the second day of his UK tour was marred by the arrest of five men by police investigating a suspected plot to harm the Pope, sources said.
Scotland Yard officers swooped after information emerged that he could be in danger.
Earlier, speaking at St Mary's University College in Twickenham, south-west London, the Pope said: "I wish to add a particular word of appreciation for those whose task it is to ensure that our schools provide a safe environment for children and young people."
He said the life of faith can "only be effectively nurtured when the prevailing atmosphere is one of respectful and affectionate trust".
"I pray that this may continue to be a hallmark of the Catholic schools in this country."
The men were arrested by officers from the Met's Counter Terrorism Command shortly before 6am.
A Metropolitan Police spokesman said a business premises in central London was being searched, as well as homes in north and east London.
The Pope continued with his engagements, unaffected by the developments.
Addressing a crowd of about 4,000 youngsters at St Mary's, the Pope warned against the limitations of both celebrity and science.
He said celebrity and riches could not bring happiness and continued: "The world needs good scientists, but a scientific outlook becomes dangerous and narrow if it ignores the religious or ethical dimensions of life, just as religion becomes narrow if it rejects the legitimate contribution of science to our understanding of the world."
In his third speech of the day in Twickenham, the Pope called for respect for the "freedom of worship" and the "freedom to follow one's conscience" without suffering persecution.
He said: "When such a respect and openness has been established, peoples of all religions will work together effectively for peace and mutual understanding."
He said there was a need "not only for theological exchange but also for sharing our spiritual rituals".
He continued: "Let me assure you that the Catholic Church follows the path of engagement and dialogue out of a genuine sense of respect for you and your beliefs."
A multimillion-pound operation is in place to protect the Pope during his tour of Scotland, London and the West Midlands, with thousands of officers involved.
The pontiff is also protected by members of the Swiss Guard.
He often travels in the Popemobile, which has a bulletproof glass enclosure.
The Vatican abandoned the use of an open-topped vehicle after the assassination attempt on Pope John Paul II in 1981.