Bishop Magee was private secretary to three popes
The Pope has accepted the resignation of an Irish bishop found to have mishandled allegations of clerical sex abuse in his County Cork diocese.
Bishop John Magee stepped aside in March 2009 after an independent report found his Cloyne Diocese had put children at risk of harm.
"I take full responsibility for the criticism of our management of issues in that report," he said on Wednesday.
The 2008 report cited an inability to respond appropriately to abuse claims.
It was conducted by the National Board for Safeguarding Children in the Catholic Church in Ireland (NBSC), a body set up by, but independent of the Catholic Church.
The inquiry was separate to last year's Murphy report on decades of abuse mishandling in the Dublin archdiocese and the Ryan report, which detailed physical and sexual abuse at Catholic-run orphanages and industrial schools in the Irish Republic.
Bishop Magee was born in Newry, County Down, and served as private secretary for three popes.
The NBSC inquiry examined how the Cloyne diocese dealt with a series of complaints of sexual abuse against two priests.
One woman reported "Father B" in 1996 as saying she had a year-long sexual relationship him and that she had seen him kissing her 14-year-old son.
Three other complaints of abuse were made against this priest between 1995 and 1997, and in 2005 a woman claimed that she had sex with the priest from the age of 13.
The conclusions of the report were a devastating critique of child protection practices in the diocese.
It said child protection practice was inadequate and in some respects dangerous as it apparently focused on the needs of the accused rather than victims.
It failed to act effectively to limit the access to children by individuals against whom a credible complaint of child sexual abuse was made.
The leader of the Catholic Church in Ireland, Cardinal Sean Brady, said he wanted to acknowledge Bishop Magee's "long and varied ministry".
"I assure him of my prayers at this time and wish him good health in his retirement," he said.
"However, foremost in my thoughts in these days are those who have suffered abuse by clergy and those who feel angry and let down by the often inadequate response of leaders in the church."