He initially stayed on in his post, but that year after a further allegation was made, and has remained off work while.
Mr Matheson said he had uncovered "clear deficiencies" in the SPA's decision-making process which he described as "completely unacceptable".
The letters also said the chief constable was "ready and willing to return to full operational duties" and under the terms of his special leave could come back with 14 days' notice - but "would prefer to do so consensually, in implementation of the decision of the SPA board".
Mr Gormley was travelling from his Norfolk home back to Scotland when he was contacted by Andrew Flanagan, the SPA's then chairman, and told to turn around. They said the chief constable was "surprised" by the move and the justice secretary's "apparent intervention", which they advised him was "unlawful".
"Key parties had not been consulted", said Matheson.
He told Holyrood that the impact Mr Gormley's return could have on those who had made the allegations against him had not been considered by the SPA.
A Scottish Government spokeswoman said: "As the Cabinet Secretary made clear, his concerns centred on the process that had been followed by the SPA and not the outcome".
Tory MSP Margaret Mitchell, who is convener of Holyrood's justice committee, said Mr Matheson's position would be "untenable" if he had intervened.
The justice secretary is to update MSPs on the future of Police Scotland's chief constable amid claims he illegally blocked his return to work.
Mr Gormley's lawyers also told MSPs that the complaints against him were "entirely denied", and were "vexatious, opportunistic and are being strenuously defended on his behalf".
"It is hard to understand how a decision could be made to for the Chief Constable to return without first confirming that doing so would not undermine the independent investigations, or the confidence of staff engaged in that process", he told MSPs.
The former Justice Secretary stated: "It's now suggested that investigations have exonerated Phil Gormley".
Speaking following today's Parliamentary statement and questions, SPA Chairwoman Susan Deacon said: "The conduct issues relating to the Chief Constable remain live and ongoing, and it remains inappropriate for SPA to offer public comment".