The allegations resulted in an inquiry into child sexual abuse known as the Ferns Report.
Dr Comiskey resigned over claims that he did not report allegations that Fr Sean Fortune had abused a number of children while Dr Comiskey was in control of the Ferns diocese.
Fr Fortune was a serial paedophile with a manipulative personality and Dr Comiskey admitted he found him difficult to deal with.
Fortune died by suicide while on bail.
Abuse 'wasn't unique to Ferns' - O'Gorman
One of his victims was the advocate and former Director of Amnesty International Ireland, Colm O'Gorman, who subsequently founded the charity One in Four for victims of abuse.
Mr O'Gorman was one of the first of Fr Fortune's many victims to report the assaults to gardaí.
He said that he hopes that Dr Comiskey will not be "uniquely scapegoated" for "what the Ferns report revealed" following his death.
Mr O'Gorman sent his condolence to Dr Comiskey's "family and friends and all who loved him".
He said that the Ferns report was "clear" and that people can read about the "appalling mismanagement in many ways of clerical child sexual abuse in the diocese of Ferns".
However, he said it is important to acknowledge that this "wasn't unique to Ferns".
"This was a systemic deliberate cover up of the rape and abuse of children perpetrated by the clergy that was directed and mandated by the Vatican," said Mr O'Gorman.
"It’s really important as we look back on that legacy that we don’t see this in terms of Brendan Comiskey having failed to manage cases.
"He didn’t fail to manage cases. He managed them in exactly the way he was required and directed to by the Vatican.
"He’s responsible for that. He’s responsible for his own actions, for his decision to comply with the cover up."
Mr O'Gorman said that the responsibility for the "global cover up" lies with the Vatican.
"There was nothing unique about Ferns. It was frankly, atypical of what we saw and what we have seen revealed in dioceses not just across this country but across the world," he said.
He added that "we have a way to go yet before we have a full and frank acknowledgement of the truth".
Mr O'Gorman said the Vatican "has never acknowledged that the cover-up was global and the cover up was directed, that bishops did as they were mandated and ordered and required to do."
"Truth still matters and we haven't quite gotten there yet," he added.
Born in August 1935, Dr Comiskey was originally from Clontibret in Co Monaghan.
He was ordained a priest of the Congregation of the Sacred Hearts of Jesus and Mary in 1961.
He became Auxiliary Bishop of the Archdiocese of Dublin in 1979 and was appointed the Bishop of Ferns in April 1984.
The Ferns report found that the former bishop failed to establish sound child protection measures in the diocese.