referee head honcho Hugh Dallas has resigned from the sfa.
The former World Cup referee was the subject of an internal disciplinary hearing on Thursday evening.
SFA chief executive Stewart Regan investigated reports of an email sent from Dallas's SFA account when the Pope visited Scotland on 16 September.
And, on Wednesday, a Catholic Church spokesman called on the SFA to act.
BBC Radio 5 live is reporting that three other SFA staff members have been dismissed, with formal warnings issued to three more.
The Catholic Church urged Scottish football's governing body to sack Dallas if it was proven he had sent the email.
Following Regan's investigation, the former referee was said to be taking a few days out to consider his future and the SFA added that it would not comment until that process was completed.
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It was sent from the SFA account belonging to 53-year-old Dallas, contained no text but included an image attachment of a school crossing sign with a silhouette of an adult holding a child's hand and the word "caution".
Beneath the road sign were words making reference to the Pope's arrival in Scotland.
While Regan was said to have returned to his Yorkshire home, SFA president George Peat said he could not comment on Dallas's departure.
"Stewart Regan has interviewed a number of people at Hampden," he told BBC Scotland.
"I have not been in there today. I stayed away from there because, if he has dismissed anyone, any appeal from people who have been dismissed would come to me.
"I don't know if people have gone or not - that is possible.
"Some people have phoned me and told me that five have left, but I don't know how many have gone and who they might be. I don't want to get involved."
Dallas, who had been the SFA's head of referee development since June 2009, had also been under pressure in recent weeks following criticism from factions within Scottish football directed at match officials.
Celtic, in particular, had been angered by referee Dougie McDonald's decision to overturn his own award of a penalty against Dundee United on 17 October.
The SFA launched an investigation after assistant Steven Craven resigned as a result of the furore and McDonald was warned for giving a false explanation for his decision.
Craven accused Dallas of "bullying and harrassment" over the incident, although that was strenuously denied by both the referees' chief and McDonald.
Although Regan promised an overhaul of referee discipline, Celtic continued to call for tougher action taken against McDonald, with chairman John Reid calling on the referee to resign or be sacked.
Reid alluded to what he claimed was a history of bias against Celtic and supported MP Pete Wishart's suggestion that referees should reveal which football teams they support.
Celtic had also recently written to the SFA asking for clarification over a penalty awarded against them by Willie Collum during the Old Firm derby against Rangers.
Following that incident, striker Gary Hooper suggested that referees wanted to give decisions against his club.
Then, this week, Scotland's referees withdrew their labour ahead of this weekend's fixtures, complaining of undue pressure, abuse and that their integrity was being questioned.
Both Dallas and the SFA were unavailable for comment tonight. The SFA have made no official comment all day despite both Polish and Portuguese officials withdrawing their offers to cover for striking refs.
One of the striking category one referees, John McKendrick, described the departure of Dallas as a "very dark day for referees in Scotland".
"We have to remember that Hugh Dallas was a world-class operator," he said.
Pictures of Dallas, crouched on one knee with blood streaming from a head wound, are one of the most stark images in Scottish football.
In 1999, during a title decider in which three players were sent off and a penalty was awarded to Rangers, Dallas was struck on the head by a coin thrown from the Celtic section of support.
Celtic subsequently hired a behavioural psychologist to investigate Dallas's behaviour in the match.
Dallas was awarded an MBE for services to football a few months after being chosen to be the fourth official at the 2002 World Cup final.