Martin Baucutt, the federation's competitions manager, said the rule had been in place for a number of years and was implemented at the request of the region's clubs.
Removing goal difference meant stronger teams could start different players or take other measures against weak teams without being punished, he said.
"We try to stop teams going out and thrashing other teams, like 20-nil every week. It's just to do enough to win, basically."
But one parent whose 11-year-old son plays soccer said the rule was unfair and punished success.
"It doesn't affect us, because we're out of the running. But there's one team that it probably will affect - and they've only let one goal in all season," said the man, who asked not to be named.
"And those kids have played really well not to let any goals in. And they should get a pat on the back. Not just, oh well, let's give everyone a trophy."
Kevin Fallon, director of football at Mt Albert Grammar and coach of Eastern Suburbs AFC, said no matter the grade, winning and losing was part of the game.
"We want to win, we want to strive to win. I think in the real world, eventually you've got to toughen up and compete.
"I just think that our game is being taken over these days by people who live in cloud cuckoo land."
Mr Fallon, father of All White Rory Fallon, said a switched-on coach could make players feel successful even in defeat.
"There's always successes, even in disaster. Somebody always plays well, some aspect of your game can be praised."
FAIR PLAY?
* Teams in the youth grades (9 to 17-year-olds) in Auckland who finish the season in the top position equal on points will be awarded joint championship winners.
* Goal difference tally will not count, as it does in senior competitions.
* Soccer bosses say rule removes some incentive for strong teams to thrash weaker ones.
