In recent weeks, the Vatican has been trying to contain damage as a string of scandals over sexual abuse of children by priests has hit Ireland, Germany, Austria and the Netherlands.
"You have suffered grievously and I am truly sorry ... I openly express the shame and remorse that we all feel," he said in an unprecedented letter covering sexual abuse of minors by clergy in Ireland.
The letter, addressed to the people, bishops, priests and victims of abuse in the overwhelmingly Catholic country, did not make any specific reference to the scandals rocking Churches in other countries, particularly the pope's native Germany.
"I can only share in the dismay and sense of betrayal that so many of you have experienced on learning of these sinful and criminal acts and the way the Church authorities in Ireland dealt with them," he said.
But the pope did not address widespread calls in Ireland for a radical restructuring of the church there nor did he say that bishops implicated in the scandal should resign.
The pope announced what is known as an "apostolic visitation" of "certain" dioceses, seminaries and religious orders in Ireland.
An apostolic visitation is an inquiry in which inspectors meet bishops, seminary or convent directors and local church officials to review the way matters were handled in the past, to suggest changes and decide possible disciplinary action.
The pope said details of the investigation would be announced "in due course."
Benedict singled out Irish bishops for criticism of their handling of abuse cases in the past.
"It must be admitted that grave errors of judgment were made and failures of leadership occurred. All this has seriously undermined your credibility and effectiveness," he said.
He added: "Only decisive action carried out with complete honesty and transparency will restore the respect and goodwill of the Irish people towards the Church to which we have consecrated our lives," he said.
Document follows damning report
The letter, the first papal document devoted exclusively to pedophilia, follows a damning Irish government report on widespread child abuse by priests in the Dublin archdiocese.
The Murphy Report, published in November, said the church in Ireland had "obsessively" concealed child abuse in the Dublin archdiocese from 1975 to 2004, and operated a policy of "don't ask, don't tell."
The latest scandal in Germany is especially delicate for German-born Benedict, Munich's bishop from 1977 to 1981.
With public opinion in Germany boiling as more cases of abuse emerge, the vice president of the Bundestag lower house, Wolfgang Thierse, called for him to apologize on behalf of those responsible.
Last week the head of Germany's Catholic Church apologized to victims of child abuse by priests when he came to Rome for a routine visit that was transformed into a crisis management meeting.
Archbishop Robert Zollitsch, head of the German Bishops' Conference, briefed Benedict about the situation in Germany, where more than 100 reports have emerged of abuse at Catholic institutions, including one linked to the prestigious Regensburg choir run by the pope's brother from 1964 to 1994.