This followed the revelation that his diocese in 1993 had provided Irpounds 27,500 to a curate, Fr Charles Payne, based at Sutton in Dublin, to reach an out-of-court settlement with a former altar boy who alleged he was sexually assaulted by the priest.
"If people have been misled by what I said [in a statement in May] I most sincerely apologise. It was not my intention to mislead, it was not my intention to cover up," he said.
"I have acknowledged since that I may have to qualify that in the future. My deepest concern has been first of all the protection of children, and secondly the care and pastoral care that is required to help people to overcome the trauma ..."
Speaking on Irish radio, he said legal constraints linked to possible criminal prosecutions meant he was fighting his case "with one arm tied behind my back".
Alluding to claims that Fr Payne's alleged victim was urged to give a verbal commitment to silence when the settlement was made, Dr Connell said the boy was still free to bring a civil or criminal case against the diocese.
The Archbishop said his statement in May that "church funds are not used in any way to make settlements of that kind - the offending priest must find his own resources", had been an attempt to "send a signal to the priests of the diocese" that it would not be acceptable for them to expect the diocese to pay for such settlements.
He qualified this by saying that where the victim had been seriously injured, the church's "mission of justice and charity" meant he would have to "come to the rescue".
He insisted he had given the payment as a loan and not as a church payment of compensation, and had not dealt directly with the priest involved. Dr Connell said Fr Payne was now in "some place we are not speaking about".
Dr Connell conceded that past failure to deal with offending priests meant the church had colluded in criminality. But he said: "We have learned from a very, very painful experience to change the way in which we deal with matters."
A church spokesman said yesterday that the secretary of the Vatican's Congregation of Bishops, Archbishop Jorge Mejia, had discussions on controversies affecting the Irish church over the weekend with both Dr Connell in Dublin and with Cardinal Daly, the Catholic primate, in Donegal. But he stressed the main reason for his visit had been to officiate at the ordination in Letterkenny of the new Bishop of Raphoe, Philip Boyce.
Meanwhile, the Bishop of Ferns, Brendan Comiskey, who last month left his post on a three-month sabbatical, confirmed he was receiving treatment in the United States for alcoholism. Rebutting press speculation that he had been forced out, he stressed the decision to go had been his.
Bishop Comiskey has been at the centre of controversy since June after challenging the Vatican to allow a debate on its rule of priestly celibacy.
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