While the report, which contains claims of bad practice and unlawful behaviour, dates back to 2014, details of it only emerged on Monday ahead of a BBC Scotland documentary.
Answering questions from MSPs at Holyrood yesterday Mr Matheson said he had only found out about it then, as the original document was an internal report produced by the national police force. But he said it had been a “mistake” for it not to have been shared with watchdogs at the Scottish Police Authority (SPA).
The SPA is now seeking “urgent assurances” from police chiefs about the issues raised in the documentary titled A Force In Crisis.
A BBC Scotland investigation claimed drafts of the report show the chief constable’s office wanted negative comments deleted, tenses changed to suggest problems had been fixed, and an entire section, where frontline officers described working in a culture of fear, removed.
It also said early drafts of the report had detailed officers conducting unauthorised surveillance, threatening and intimidating witnesses, unlawfully detaining suspects, colluding while compiling statements and failing to reveal evidence, but these allegations were removed from the final version.
Tory justice spokesman Liam Kerr raised the matter with the Justice Secretary, telling him: “This is a scandal and I do not use that world lightly.
“It appears that the head of our national police force has engaged in a deliberate cover up of allegations of corruptions, and changed the tenses of other problems to suggest they were already fixed.”
Labour justice spokesman Daniel Johnson hit out saying: “What does it say about the organisation’s culture and ethos that these were some of the very first acts of the chief constable?”
He pressed Mr Matheson on when he first knew about the allegations, demanding to know if it was before the programme was screened.
The Justice Secretary said: “The nature of the report which the BBC published was brought to my attention when they published information relating to their programme and the fact that they were focusing on this particular report.”