The leader of 1.2bn Catholics worldwide said a goal of full unity between the two churches “may seem distant” but it remained an aim that should direct “every step”.
He said progress towards full unity would not be the result of human actions alone, but would be a “free gift of God”.
“Beneath his merciful gaze, we cannot claim that our division is anything less than a scandal and an obstacle to our proclaiming the Gospel of salvation to the world,” the Pope told Archbishop Justin Welby.
“Our vision is often blurred by the cumulative burden of our divisions and our will is not always free of that human ambition which can accompany even our desire to preach the Gospel as the Lord commanded.”
The archbishop’s visit to Rome, which began on Saturday, focused on work by the churches to eliminate human trafficking and modern-day slavery.
Archbishop Welby described human trafficking and slavery as “a grave crime” against humanity.
He also praised the Pope’s “remarkable” care for the poor and suffering, and his “passion” for reconciliation, witnessed recently in his Middle East visit. He said he hoped the collaboration with Pope Francis would lead to an “effective challenge” to the “unspeakable disasters of war and conflict” throughout the world.
Archbishop Welby, who gave a gift to the Pope of a cutting from a fig tree in Lambeth Palace planted by the last Roman Catholic archbishop of Canterbury, Cardinal Pole, added that the Church of England remained “deeply committed” to ecumenical talks.
But: “I realise that there are matters of deep significance that separate us.”
The meeting comes as the General Synod is expected to approve next month the introduction of woman bishops in the Church of England. The Roman church does not allow women to become priests.