Both men resigned in 2014 after a series of allegations were made by garda whistle-blower Sgt McCabe in 2007 and 2008.
Sgt McCabe made a series of complaints about garda conduct of investigations.
Mr Callinan denied any wrong-doing when the allegations were made.
The report identified serious flaws and failures in criminal investigations, but found no evidence of garda criminality or corruption.
The 349 page report by the former High Court judge, Kevin O'Higgins, describes Sgt McCabe as a "dedicated and committed" member of the force who acted out of genuine and legitimate concerns about garda behaviour in his division and Bailieboro Garda station.
The judge rejected Mr McCabe's allegations of corruption against the former commissioner, calling them "hurtful".
He also said some of Sergeant McCabe's complaints against the force were over-stated and exaggerated.
Sgt McCabe made a series of complaints, alleging there were cover-ups of wrong-doing, and said the force, as an institution, had closed ranks against him.
Mr Callinan, who has been vindicated, denied all claims when the allegations were made.
The report also found that the former Justice minister Alan Shatter had handled the sergeant's complaints in an "appropriate manner."
In his report Judge O'Higgins criticises garda handling of several investigations carried out by officers in Bailieboro saying they were very poor as they were carried out by probationary members of the force and were not properly supervised.
He says there were unnecessary delays and errors in some of the investigations and flawed disciplinary were followed after the complaints were made.
While the report clears the former commissioner and the former justice minister, it serves to highlight problems in the Irish police force at a time when its critics say it requires strong leadership, modernisation, reform and better resourcing.
In 2014 the Garda Inspectorate, an oversight body, released a report which described the force as "broken."
An inquiry into alleged garda wrong-doing in Cavan/Monaghan has cleared the former Justice minister Alan Shatter and the former Garda (Irish Police) Commissioner Martin Callinan.