A meeting of the General Synod was disrupted when a man, described by the Church of England as having "personal health issues", was arrested for allegedly assaulting two stewards.
A spokesman for the Church said a man was asked to wait as the Archbishop of Canterbury Justin Welby and the Archbishop of York Dr John Sentamu moved in procession to the front of York Minster. He reportedly then lashed out, leaving a member of Dr Sentamu's staff Dave Smith requiring treatment from ambulance staff.
The police said they responded within minutes of being called, and arrested a 42-year-old man on suspicion of assault.
The Church later said the man was not a protester, and said in a tweet that he was a "local man with personal health issues and known to police". It asked followers to "please pray for him".
The worrying breach in security came as members of the Church's national assembly are today expected to formally endorse an apology over clerical child abuse.
The Synod will be asked to back an apology issued by Mr Welby and Dr Sentamu over failings in procedures to protect children, young people and adults from physical and sexual abuse by clergy and others.
The apology also covers the "failure to listen properly to those so abused."
The debate at the University of York comes after a final report was published in May into the operation of child protection policies following a series of scandals involving clergy within the Diocese of Chichester.
The report comes after the former Archbishop of Canterbury, Dr Rowan Williams, now Lord Williams, ordered an inspection of the diocese in December 2011.
At the time the report was published, the Most Rev Welby renewed his apology to the victims of clerical abuse for their "pain and hurt".
The Government's welfare reform programme - and whether to back a call rejecting the "misleading characterisation" of all welfare recipients as "scroungers" will also be debated by General Synod members.
A briefing document drawn up for the General Synod by Philip Fletcher, chairman of the Church's Mission and Public Affairs Council, has accused Government spokesmen of making "political capital" out of presenting unemployment as a "strivers" versus "scroungers" debate.
The Most Rev Welby and Dr Sentamu, backed a letter to the Daily Telegraph earlier this year criticising the Government over benefit cuts.
The letter, signed by 43 bishops, opposed to a 1% cap on benefit rises saying this could push 200,000 children into poverty.
Additional reporting: PA