The Archbishop of Canterbury and Pope Benedict XVI have publicly acknowledged that "serious obstacles" stand in the way of their Churches' cooperating.
Dr Williams and the Pope agreed to address materialism
Dr Rowan Williams, the leader of the worldwide Anglican Church, is on a short visit to Rome.
In a joint declaration, they said it was a matter of urgency that talks continue on issues which divide them.
It comes amid concerns in the Roman Catholic Church over possible women bishops and gay Anglican bishops.
The Common Declaration was signed by Pope Benedict and Dr Williams during a formal audience at the Vatican.
"Our long journey together makes it necessary to acknowledge publicly the challenge represented by new developments which, besides being divisive for Anglicans, present serious obstacles to our ecumenical progress," it read.
"It is a matter of urgency, therefore, that ... we also commit ourselves in our continuing dialogue to address the important issues involved in the emerging ecclesiological and ethical factors making that journey more difficult and arduous."
The statement also called for the two churches to stand together over issues including the "pursuit of peace in the Holy Land" and the "negative effects of materialism".
It made a commitment to talk to other religions and "reach out to our non-Christian brothers and sisters".
The Vatican declaration comes only a few days before the Pope leaves for Turkey to address problems caused by another deep division among Christians - between Rome and the Orthodox Churches, dating back almost 1,000 years.
After the formal audience, the religious leaders shared worship together at the Vatican.
Earlier they had held a private 15-minute meeting.
Speaking afterwards, Dr Williams said it had been a "very warm meeting" and stressed the importance of his relationship with the Pope.
"I think if we are not able to understand where each other is coming from in terms of our thoughts about God, our thoughts about the church, our thoughts about our vocation, then really a great deal of the negotiating and the fine detail and fine tuning has been a waste of time.
"I think we need to understand each other as fellow pastors and fellow teachers in the church. I think this morning is a great step towards that."
Dr Williams was expected to spend most of Thursday inside the Vatican city.
It is thought he will give two lectures - one at the Vatican's Academy of Sciences - during his six-day tour.
The Roman Catholic Cardinal, Archbishop of Westminster, Cormac Murphy O'Connor is thought to have accompanied Dr Williams on the visit.
This latest meeting was intended to mark the 40th anniversary of the meeting between their predecessors, Dr Michael Ramsey and the late Pope Paul VI, at the Holy See.
The ordination of Gene Robinson - a divorced man in an openly gay relationship - as the Bishop of New Hampshire in the US in 2003 was viewed with "concern" by the Catholic Church.