The four-volume report uncovered no evidence to show senior police officers tried to block child abuse investigations.
It also found Detective Inspector Peter Fox - who alleged the cover up - was not a credible witness, and it was appropriate for police to instruct him to stop his own investigations.
"Fox gave evidence that was untruthful," the report said.
"The Commission formed the view that Fox had engaged in conduct that was inconsistent with the integrity required of a police officer.
"The Commission formed the view that Fox had developed what amounted to an obsession about both the Catholic Church and alleged conspiracies involving senior police."
The inquiry also looked at how the church handled complaints about former priests Denis McAlinden and Jim Fletcher, both now dead.
Three volumes have been released, while the fourth is confidential.
It also made adverse findings against Father William Burston and Monsignor Allan Hart, and found senior church officials did have information relating to child sex abuse that would have assisted the police.
"Each was found to be an unimpressive and/or unsatisfactory witness in some respects," the commission, headed by Margaret Cunneen SC, found.
The special commission of inquiry was announced by NSW Premier Barry O'Farrell in November 2012, following explosive allegations made to the media by Det Insp Fox.
He alleged the Catholic church had covered up evidence about pedophile priests in the diocese of Maitland-Newcastle in the Hunter region of NSW.
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