Prepared by the bishops' conference in association with the Scottish Safeguarding Service, the report said a total of 46 allegations were reported, of which 55% related to sexual abuse, 19% to physical abuse, 11% were allegations of verbal abuse and 15% were in connection with emotional abuse.
Of those accused, 56% were priests, 22% were volunteers, 11% were parishioners and the remainder were staff or other people connected to the Church.
The Church said there have been no prosecutions in relation to 61% of all cases reported. Of the rest, 15% resulted in a prosecution, 10% are still under investigation and the remaining 14% are described as "unknown historical cases".
The audit report revealed that the ministry of almost a quarter (24%) of those accused had been restricted.
Archbishop Philip Tartaglia, president of the Bishops' Conference, said: "We recognise the trauma and pain that survivors of abuse have suffered and we are committed to providing for them both justice and healing."
He added that 2013 had been "a test of faith" for Catholics but the Church was committed to "consolidation of our safeguarding practices, the renewal of trust in our unshakeable commitment to atoning for abuse in the past, guarding against abuse in the present and eliminating abuse in the future, and supporting those who have been harmed", the Scottish Herald reported.
On average, half of all complaints made to the Church each year between 2006/12 were historical, dating from before the year 2000, the audit report said.
A review of all historical allegations of abuse from 1947 to 2005 will also now be carried out.
The full text of the report can be read here.