Farry was forced to respond after the unexpected resignation of Jim McGilvray, a Grade One official. And, tongue in cheek, Farry pleaded guilty to McGilvray's charge that the SFA's guidelines for officials are creating "robots with whistles".
McGilvray, from Edinburgh, resigned after 11 years as a top-ranked referee in Scotland. He told a newspaper that the "final straw" was feeling forced to book Paul Gascoigne for celebrating after scoring the first of his two goals in Rangers' 2-1 win against Partick Thistle at Firhill on 3 February.
McGilvray alleged that other officials in Scotland feel restrained, and was quoted as saying: "Referees are running scared of a system which is flawed in so many areas."
But Farry said: "I would not anticipate that this resignation will spark an exodus of Scottish referees. We are proud of the standard of our referees and will continue to work assiduously to maintain that standard.
"If the SFA is being accused of creating robots by issuing instructions then we plead guilty - the set of instructions is called the laws of the game."
Farry said that the SFA accepted McGilvray's resignation with reluctance, and said that the decision could have been brought about by the stresses and strains faced by officials, who earn just pounds 130 to take charge of a top game.
McGilvray, 47, had been a referee for 21 years. He said that he decided to give up after having to book Gascoigne for celebrating almost forced him to send off the England player later in the match. He also dismissed two Partick players - Rod McDonald and Billy McDonald - in the same match.
Two other Scottish referees, Dougie Smith of Troon and Willie Young of Clarkston, have been involved in disputed yellow card incidents with Gascoigne this season.
Smith was accused of lacking a sense of humour when he booked Gascoigne, who pretended to "book" the referee when he handed back a yellow card the official had dropped in a game against Hibernian. Young was criticised when he booked Gascoigne for celebrating a penalty award against Motherwell.
Before Farry's statement, an SFA spokesman said McGilvray's decision to resign was a by-product of the "pressures of the modern game" and the heavy scrutiny of officials by the media. "I can confirm a letter has been received giving intimation of his resignation," the spokesman said.
"The Association is sorry to receive it, as we always are in such cases. Resignations are not unusual over the course of a season, but perhaps it is indicative of the pressures faced by referees in the modern game.
"They are under fierce scrutiny. They are not alone in that regard, as so are players, managers and club chairmen. People have to live with such pressure and adapt under the circumstances."
The Scottish League will fill the vacancy left by McGilvray, who was due to take charge of Stenhousemuir versus Stranraer in the Second Division on Saturday and a Premier Division match between Motherwell and Falkirk the following week.
Another official, George McGuire of Bonnyrigg, is considering legal action against the SFA after being downgraded to amateur status for his role as a linesman in the match between Rangers and Hearts in October.
n BBC Scotland will show the Scottish Cup quarter-final tie between Celtic and Dundee United on 10 March, while Sky Sports will show St Johnstone versus Hearts on 7 March.
SCOTTISH CUP QUARTER-FINALS Revised draw: Thursday 7 March: St Johnstone v Hearts. Saturday 9 March: Aberdeen v Forfar Athletic or Airdrie; Caledonian Thistle v Rangers. Sunday 10 March: Celtic v Dundee United.Reuse content