A newspaper report at the weekend claimed the SFA's head of referee development had used his work e-mail to forward on a "tasteless message" about the Pope's visit to Glasgow.
SFA chief executive Stewart Regan confirmed he launched his own investigation.
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Hide AdIn a statement, he said: "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."