The Archbishop of Dublin, Dr Diarmuid Martin, said yesterday that the Pope in making his apology was genuinely upset at the reaction to his comments which were taken out of context.
Speaking to journalists in Dublin, Dr Martin said he watched the Pope making his statement that morning.
"He expressed his regret very, very clearly. Again, he expressed what was the real sentiment of what he said. It was clear that he was visibly upset by what happened," Dr Martin said.
The archbishop said he was beginning to see around the world a growing tendency that one took what the Pope said in the broad context of what he intended - which was an invitation to dialogue and a rejection of violence.
"I think what's most important now is to ensure that the reactions are calm and that people genuinely see that the Pope never intended to offend people by what he said," Dr Martin said.
"I would hope that people who heard him will see exactly what his sentiments are and that they will respect his genuine sense of regret that what he said was interpreted in that way."
The archbishop said what struck him was that the Pope made the comments on Tuesday and there was absolutely no reaction to what he said. Those who heard the entire discussion understood the context.
However, when a particular phrase was taken out of its context and almost attributed to the Pope - whereas he in fact said this never reflected his own meaning - reactions like that could take place.
"The important thing is to move forward. He has appealed for frank and open dialogue and that's the important thing we should all be moving towards at this stage," he said.
Dr Martin said he hoped Irish Muslims would understand that the Pope's intentions were positive. "It was a text about dialogue and I would like to see greater dialogue. We've got a good and important Islamic community in Ireland and relations here have been very, very good."
He had met the leaders of the Islamic community in Dublin on many occasions, said Dr Martin. Sometimes it was when tensions appeared the health and strength of dialogue could be seen best.
"I hope those who are in a leadership position and looking at the comments of Islamic leaders in the last two days . . . say look, judge this on what happened in the broad context and let's get back to this dialogue as it's very important . . . to get back to the other point that the Pope was stressing, namely that religious leaders should be working together in the face of a culture that rejects a role for religion in any society," Dr Martin said.
"If you watched him during the Angelus this morning, you can see that he was genuinely upset that this has been the reaction," he said.
The Pope very clearly said this text was not his thought in any way and did not reflect his attitude and he was just showing a particular historical context.
"His spokesperson has expressed his regret, the cardinal secretary of state has expressed his regret and today the Pope himself has very clearly and very emotively shown that regret," the archbishop said.