James Bee, chairman of the Scottish Senior Football Referees Association agreed to a media release criticising the SFA Disciplinary Tribunal for handing a two-match ban to Dundee United striker Nadir Ciftci.
The 21-year-old was handed the suspension on Tuesday following an incident involving match official Gavin Harris during October's League Cup clash with Inverness Caley.
Ciftci was initially accused of "seizing hold" of Harris "by the throat" after being sent off following a brawl involving several players from both teams, but the 21-year-old was later charged with "placing an open hand into the lower area of the assistant referee's throat" on the basis of video evidence.
A SSFRA spokesman said: "We wish to express our deep dissatisfaction at the leniency of the sanction imposed by Tuesday's Disciplinary Tribunal on a player who was found guilty of physically abusing one of our members.
"As an association, we feel this sends out completely the wrong message on issues surrounding the protection of match officials at all levels of the game in Scotland.
"We will be seeking talks with the Scottish FA within the next few days to discuss matters before reporting to our members."
But the SFA has condemned Bee and his members for venting their anger through the media.
"The Scottish FA has yet to receive any formal correspondence from the Scottish Senior Football Referees' Association despite being made aware of a statement issued with the authority of its chairman, James Bee, via the media," the SFA statement read.
"It would have been befitting of a members' organisation such as the SSFRA to seek an explanation for the outcome directly, without the need for such inflammatory media comments.
"Notwithstanding the lack of communication, we have forwarded the reasons of the judicial panel to Mr Bee for his consideration."