The Co Armagh parish of Drumcree was acting in complete defiance of the General Synod of the church, a spokesman for the Church of Ireland has said.
The comment came hours after two Union flags were erected yesterday on the tower of Drumcree church, in apparent contravention of a ruling made at a recent meeting of the Church of Ireland Synod in Dublin.
The spokesman said it now appeared the rector and select vestry of Drumcree were "almost daily doing all they can" to defy the ruling body of the Church of Ireland.
The Drumcree situation, the spokesman continued, had caused "personal pain over four years to Archbishop Eames" and there was a belief among many members of the church that something had to be done to heal the rift in the Church of Ireland.
The ruling on flags arose following a debate on a report on sectarianism at this year's General Synod which met at the Royal Hospital Kilmainham. The Synod passed a motion on May 18th which stated: "The only flags specially authorised to be flown on church buildings or within grounds of the Church of Ireland are the cross of St Patrick, or alternatively, the flag of the Anglican Communion bearing the emblem of the Compassrose".
The motion went on to say: "Any other flag flown at any other time is not specifically authorised by this church."
However, the rector of Drumcree, the Rev John Pickering, denied that his parish was in contravention of the General Synod ruling regarding the flying of the Union flag.
Mr Pickering referred to a Church of Ireland press release dated May 21st this year which stated that the Synod had not in fact banned the flying of the Union flag in the North.
"In that press release, Dr Eames condemned media reports which claimed that national flags had been banned as wrong, misleading and mischievous", Mr Pickering said.
"The church did not ban the flying of the Union flag. Instead it recommended that flags flown should have a religious rather than a political theme. The May 21st press release makes the position quite clear. The inference that Drumcree parish is in contravention or defiance of a church ruling is incorrect," Mr Pickering said.
Meanwhile, it is expected that the security forces will move into the fields adjoining Drumcree church within the next 24 hours. There has been a steady build-up of both police and army personnel in Portadown in recent days. Heavy armoured military vehicles have also been seen arriving at the town's Mahon Camp. Metal screens were erected yesterday on Portadown's Northway close to the nationalist Obins Street flats on the outward Drumcree parade route where there have been recent clashes during Orange Order protest parades.