The cacophony of boos and jeers which rung around Hampden rendered it impossible to hear the tune or the words sung by the England team and more than 5,000 visiting supporters.
Given that it was the British national anthem being played - not the English national anthem, as the match programme stated - the reaction of the Scottish fans has led to critics.
Keegan would not publicly be drawn beyond expressing his "disappointment" at the amount of booing, which was the loudest that many observers had ever heard inside a sporting arena during a national anthem.
The England coach routinely issues an appeal before matches at Wembley over the public address system for the visiting team's anthem to be respected by home supporters.
But he felt the need to issue a public statement three days before the game urging restraint from England fans to ensure the Scottish players are not given any extra inspiration to overturn the 2-0 deficit.
Keegan said: "While we were all disappointed by the national anthem being booed on Saturday, it did help make our players even more determined.
"So before anyone thinks about booing `Flower of Scotland' just think what it may do to their players. Please make yourself heard cheering on England rather than inspiring Scotland."
With at least one eye apparently on England's bid to host the 2006 World Cup, David Davies, the FA's executive director, said: "There will be a worldwide audience for the Wembley game, so it's an opportunity for our fans to set a good example."