Scottish Football Association chief Stewart Regan has promised an overhaul of how referees are disciplined.
It follows Dougie McDonald's admission that he lied in explaining his decision to overturn a penalty awarded to Celtic against Dundee United at Tannadice.
Regan has resisted calls for an independent inquiry.
But he suggests that a committee mostly containing former referees was not the proper body for investigating an issue with a current official.
"The investigation into events at the recent Dundee United v Celtic was effectively independent since I had only just started as chief executive and, as an Englishman, arrived with no political baggage and no hidden agenda," said Regan in an interview on the SFA website.
"Where I think there is an issue is whether a referee committee consisting largely of former referees was the correct avenue for a disciplinary case against a current referee."
The Scottish FA has to acknowledge that the process was flawed
Scottish Football Association chief executive Stewart Regan
Regan falls short of wholehearted backing of McDonald, who will continue as a referee despite calls from some quarters for him to resign.
"The referee committee made their judgment and it is now up to Dougie to learn from what has happened and use his experience to overcome the inevitable scrutiny he will undoubtedly be under when he resumes refereeing this weekend," said the chief executive.
"Dougie now has to show strength of character to recover from a very public aberration. But, in a wider context, the Scottish FA has to acknowledge that the process was flawed."
McDonald had awarded a penalty to Celtic for a challenge by goalkeeper Dusan Pernis on striker Gary Hooper but immediately decided he had made a mistake.
He consulted his assistant before starting the game with a drop ball but later admitted that he had exaggerated the role of Steven Craven in overturning the decision when explaining his reasons to Celtic manager Neil Lennon.
Craven resigned, leading to an investigation led by Regan that concluded that McDonald was correct to overturn the penalty award but issued a warning to the referee for the false explanation for his reasons.
Regan met with the SFA board to discuss the affair on Thursday
Celtic have been angered by the affair, with Hooper claiming that referees are biased against the Glasgow club, and chief executive Peter Lawwell met SFA officials on Wednesday for talks.
However, while McDonald has vowed to continue as a referee, Regan plans to initiate a wide-ranging review of the internal operations of the association.
"As I said at my media conference, it is important we separate the issue of decision making on the pitch, which was proven to be correct, and the decision making off it, which I have stated was unacceptable," he said following a SFA board meeting that discussed the affair.
"I submitted a proposal to allow me to address a series of issues that have arisen and have been given the go-ahead to proceed with it.
"Suffice to say, I will be seeking to ensure a greater urgency, transparency and openness in all future decision making.
"The association has to embrace an era of instant information and I hope to produce a suite of measures to re-establish faith in our systems."
Meanwhile, Regan said that referees would be reminded in writing about the importance of "providing accurate information at all times on and off the pitch".
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