Hugh Dallas has resigned from his position as the Scottish Football Association's head of referee development, according to reports.
SFA chief executive Stewart Regan refused to comment on the former World Cup referee's future last night and now reports claim Dallas has stepped down.
Regan launched an inquiry earlier this month after reports of the alleged email surfaced and he had little to say when questioned last night over rumours Dallas was set to depart from the SFA.
Regan said: "I'm not prepared to comment on anything relating to any members of my staff.
"We are undertaking a process at the moment and it would be unfair to make any comment on any member of staff until that process is completed."
Regan acted after reports claimed a photograph relating to the Pope's visit had been passed on via official SFA emails.
The photograph showed a road sign featuring a woman and a child with a doctored message referring to the Pontiff below.
The SFA chief executive said in a statement on November 10: "I can confirm I have looked into the circulation of the email reported in the media at the weekend.
"Let me state categorically that I do not condone the transmission of any email content that might cause offence to anyone.
"I have spoken with staff and the matter will now be dealt with internally, in line with the Scottish FA's information systems acceptable use policy."
However, days after Scotland's category one referees announced a weekend of strike action, the director of the Catholic media office, Peter Kearney, wrote to Regan demanding swift action.
Kearney wrote: "I am writing to you to express my concern at an allegation made recently against a senior official of the SFA, Mr Hugh Dallas, the head of referee development.
"He has been accused of sending an email from his SFA email account on the day of the Pope's visit to Scotland, which was totally unprofessional, gratuitously insulting to the Pope, deeply offensive to the Catholic community of Scotland, and an incitement to anti-Catholic sectarianism."
Kearney asked that the results of the internal investigation be made public and if the allegations are proven Dallas be "removed from his post".
Regan backed Dallas earlier in November after the former World Cup referee categorically refuted allegations he had bullied former assistant referee Steven Craven.
Craven accused Dallas after quitting the profession following his involvement in Dougie McDonald's decision to rescind a penalty awarded to Celtic during their victory over Dundee United last month, a decision which sparked much of the controversy that led to the referees' strike.
