Fachtna Murphy said sorry after it emerged that paedophile priests in Dublin were not pursued for their crimes because police officers often viewed Church figures as above the law.
Mr Murphy said the report into the sexual abuse committed in the Dublin Archdiocese over a 40-year period made for "difficult and disturbing reading".
"The Commission has found that, in some cases, because of acts or omissions, individuals who sought assistance did not always receive the level of response or protection which any citizen in trouble is entitled to expect from An Garda Siochana," he said. "I am deeply sorry that this occurred."
The Commissioner said the undue deference which was shown to clergy should have no place in criminal investigations and assured the public that protecting children was a priority for the current day force.
His comments come as Amnesty International called for the Government to enshrine the rights of the child into the Republic's constitution.
The human rights group said it was time for a public referendum on the issue to pave the way for necessary legislative reform.
"This report makes for deeply shocking reading, even after all that has gone before it," said Colm O'Gorman, Amnesty's executive director in Ireland.
"Bishops in Dublin colluded with child abusers, protecting them and hiding them, enabling them to prey on the innocent. Children were deliberately sacrificed to protect the Church. Dozens of priests and members of the clergy were involved."
But he said the State also had responsibility to shoulder and noted that the authorities are still deprived of many legal powers to protect children and said: "Where the State fails to defend the rights of children and abdicates responsibility for their care, then abuse and exploitation are all too often the result."
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