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The demonstrators shouted protests against Dr Robert Runcie as he ascended the pulpit of All Saints Anglican Church.
The protesters, who claim to be from the British Council of Protestants, are angry at Dr Runcie's suggestion that the Pope should become spiritual leader, or "universal primate" of a future united church.
They were eventually led away.
Outside the church, the Reverend Ian Paisley, leader of the Free Presbyterians in Ulster and his colleague Rev David McIveen revealed t-shirts saying "Christ alone is the sole head of the Church".
The demonstrations are part of an ongoing campaign against Archbishop Runcie's vision of universal primacy.
A month ago, Dr Runcie suggested in an interview for the Italian magazine "Il Regno" that many non-Catholics supported the idea of a united Christian church under the Pope's leadership.
This provoked outrage among Anglicans and Catholics.
The Rev Ian Paisley described Dr Runcie as an "ecclesiastical Judas Iscariot" and others accused the archbishop of ''betraying the Reformation'' and being a ''crypto-papist''.
Dr Runcie's historic four day visit to Rome has only increased Anglican opposition to his proposals, with Mr Paisley flying out to the Italian capital to make clear his opposition .
The Archbishop's tour has been dominated by discussions with Pope John Paul II on Christian unity but the two leaders disagree on the finer details.
Dr Runcie favours a limited spiritual papal leadership which would not involve any political or constitutional change within individual churches.
However, the Pope is adamant that the papacy should not become merely a symbolic office.
In addition to these differences, a further barrier to a workable union is the ordination of women.
The Vatican denounced the ordination of a female bishop in the US in February this year and remains firmly opposed to the Church of England's plans to ordain women priests.
After the disruption of tonight's service, the Archbishop subsequently attended papal mass at St Peter's square, becoming only the second Church of England leader to do so since the Reformation.
Dr Robert Runcie's trip to Rome came seven years after Pope John Paul II made the first papal visit to Britain since the 16th Century split with the Vatican.
The two church leaders signed a common declaration to work towards a union on the last day of the Archbishop's visit.
Both Archbishop Runcie and the Pope acknowledged that there could not be a reconciliation between the two churches while the Anglican church allowed female priests and bishops.
Dr Runcie did much to steer the Anglican Church towards accepting female priests, although he had initially worried about the effect it would have on relations with Catholics.
Dr Runcie retired in 1991. He died nine years later after a battle with cancer.
The Pope died at 2137 (1937 GMT) on Saturday 2 April 2005 after he failed to recover from a throat operation.
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