The Football Association has labelled England fans who booed Chelsea defender Ashley Cole during the 5-1 win against Kazakhstan at Wembley as "crazy".
Cole was booed after playing a sloppy pass that led to the visitors' goal.
"It is crazy that a section of our own supporters are booing one of our own players," said an FA spokesman.
But Football Supporters' Federation's Kevin Miles said: "People have paid their money and have every right to express their opinion."
The fans' treatment of Cole on Saturday was high on the agenda for manager Fabio Capello and stand-in captain Rio Ferdinand in their post-match interviews.
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The FA spokesman agreed, adding that booing individuals appears to be a feature of the new Wembley, with Cole's Chelsea team-mate Frank Lampard and Tottenham's David Bentley previous victims.
"(Booing) is clearly not going to help the team during the course of a game, and certainly not the individual being booed," they said.
"Unfortunately, we are all aware that we have had problems of this kind since we have come back to the new Wembley.
"That is why Fabio Capello stressed before the game we needed the crowd with us.
"The supporters really got behind us for the vast majority of the game, and there was a great atmosphere during the first half in particular.
"Several players have said they were encouraged to see large numbers in the crowd applauding Ashley Cole to counter-balance those booing him.
"It is unfair on all the fans who have come to the game with the best intentions of supporting the team throughout."
Miles, who is the supporters' federation's international co-ordinator, agreed that booing is rarely productive, but insisted that only a minority of fans were involved.
"I hardly heard it, though I was aware of it. It seemed to be a minority," he said.
"Once the team have gone out there and are playing, fans should do what they can to try to improve or support what they are trying to do.
"I can't imagine a situation in which a player being booed every time he touches the ball, no matter what mistake he's made before then, is going to feel more confident or lifted by the experience."
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