Dr Williams said the Pope was “most welcome” at Lambeth Palace The Pope has met the Archbishop of Canterbury at Lambeth Palace in London on day two of his visit to the UK.
The meeting with Dr Rowan Williams, the head of the Church of England, was also attended by bishops of both the Anglican and Catholic churches.
It comes at a time when Anglican moves towards appointing women bishops have unsettled relations with Rome.
But the Pope said he wanted to focus on the “deep friendship” between the two churches rather than their differences.
Later, the Pope will address MPs and business leaders in Westminster Hall.
The Lambeth Palace meeting marked the first time a Pope has met the Archbishop at his official residence.
It was viewed as an important event more than 40 years after official talks began about possible reunification of the two churches.
Divisions remain over Roman Catholic opposition to the ordination of women priests. Meanwhile the Church of England’s General Synod left the way open for appointing women bishops at its meeting in July.
The Vatican angered many supporters of women’s ordination by describing it as a “grave crime” to be dealt with in the same process as sex abuse, though it denied it was equating the two.
Dr Williams said in his opening remarks that the Pope was “most welcome” at Lambeth Palace.
He then praised the pontiff’s “consistent and penetrating analysis of the state of European society”.
Later, the speech at Westminster Hall is expected to be the most political of the Pope’s visit. He is said to be ready to talk about the important role faith must play in shaping public policy.
Pope Benedict XVI is also likely to stress the value of Catholic social teaching and link it with ideas of community-building contained in Prime Minister’s David Cameron’s concept of the Big Society.
The day will end with the Pope celebrating Evening Prayer at Westminster Abbey, before a state banquet for his entourage is held, although he is not expected to attend.
Earlier, the Pope led an assembly of 4,000 Catholic school children in west London.
He used his address at St Mary’s University College in Twickenham, to say that the safety of children was vital in all schools, an apparent reference to the Church’s child abuse scandal.
Around 300 worshippers attended the prayer service
He also warned against the limitations of celebrity and science.
The pontiff told the crowd young people were often encouraged to model themselves on celebrities.
He said: “My question for you is this: What are the qualities you see in others that you would most like to have yourselves? What kind of person would you really like to be?’
“I’m asking you not to be content with second-best.”
He went on to say having money or a successful career was not enough to make people happy, but true happiness could be found in God.
Tight security surrounded the event, called The Big Assembly.
It took place as the Metropolitan Police revealed five men had been arrested by counter-terrorism officers in central London.
Monks and nuns had waited in long queues and were frisked by police.
Around 100 protesters against the Vatican’s record on gay rights, equality and birth control had gathered ahead of his arrival, amid tight security.
The Church saw it as an opportunity to celebrate the work of more than 2,000 Catholic schools across the UK, in partnership with the state.
But critics said it could fuel hostility to faith schools and serve as a painful reminder of the child abuse scandal within the Catholic Church.
There has been a wave of cases in which Church authorities failed to deal properly with priests accused of child abuse, sometimes just moving them to new parishes.
Lord Patten, who has helped the government co-ordinate the visit, said the Catholic Church was dealing with the crisis.
He said: “For many of us, one of the worst aspects of all this was that the Catholic Church tried to hide what was going on.
“Well, I think everybody has learnt from that and learnt that institutional arrogance, the way institutions behave, can sometimes get tragically in the way of their message.”
Prior to the assembly of school children, the Pope told a gathering of religious congregations that he had particular appreciation “for those whose task it is to ensure that our schools provide a safe environment for children and young people”.
He added that the life of faith can “only be effectively nurtured when the prevailing atmosphere is one of respectful and affectionate trust”.
He also spoke of his “deep appreciation” for those who devoted their lives to teaching and paid tribute to the “outstanding contribution” made by religious orders to education.
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