Manukau City board chair Hone Fowler said the players involved weren't club members and it had decided to voluntarily withdraw from the competition. The incident was now being investigated by the Auckland Football Federation [AFF].
The Herald understands the referee returned to the game after a week's break.
Another incident saw Ranui Swanson Football club - which was already on a final warning - forced to withdraw after a member of its management accused a referee of "being a cheat". The club is appealing the decision by the Northern Football Federation [NFF].
When questioned about football referees, Ellerslie AFC chairman Tim Adams said the "number of referees has been declining over the years and now there's not enough and so now they're getting elevated into higher levels earlier before they're potentially ready".
"Although some are ready, some aren't."
Adams said the referee involved in the Manukau incident was fortunately "a strong character".
However, elevating young referees too soon did mean some were "being tested at a level you haven't done before, you make mistakes, you get abused, you get down on yourself and the cycle continues".
"So the referee abuse thing is not just 'hey, stop abusing referees', that would be good if that happened but there needs to be more of them to have a better base, better training and better ability because you're always going to get someone who doesn't agree with someone's decision."
But referring was a hard sell for clubs.
"People who have never done it before are like 'I don't want to be yelled at the whole game'."
The cost of playing football was also higher than rugby, he said.
"It's a pretty expensive sport to play. I think there's people in the lower decile areas going well, 'I'm not going to register to play for mate's team'.
"It's something that happens in football that no one really talks about, but it does happen every week."
Fowler agreed there were was a shortage of referees and some of those coming through were young. However he wanted to see a more cohesive approach in working with referees which they were currently working on with the AFF.
An executive of another Auckland football club, who did not want to be named, believed violence towards referees was more a reflection on what was happening in society in general, rather than just on the sports field.
He agreed "100 per cent" there wasn't enough referees and added "who would want to be when you get abused all the time".
In a joint statement with AFF chief executive Steven Upfold, the NFF said there were no circumstances which justified "the anti-social behavior of a small minority of players, coaches and spectators".
"The message is simple, those who cannot behave in a civilised and respectful manner are not welcome in the game and will be removed from the game."
