The Football Association of Wales has launched an investigation into the coin-throwing incident that marred Sunday's Cardiff-Swansea derby.
Referee Mike Dean, who was struck on the head by a coin at Ninian Park, has made his official report to the FAW.
An association spokesman said: "We are currently investigating the events of yesterday."
Dave Jones fears Cardiff will be punished as a result of the incident in the 2-2 draw with with Swansea.
Wirral official Dean suffered a cut forehead by what is thought to have been a coin thrown by a home supporter.
Bluebirds boss Jones said: "I hope the club don't suffer serious repercussions as it was only one person and there were 20,000 people here.
I hope it doesn't mar the occasion because it was a fantastic game of football that had everything
Cardiff City manager Dave Jones
"But we'll have to take whatever sanction they throw at us."
South Wales Police said on Monday a 24-year-old man from Pontypridd had been charged in connection with a missile- throwing incident. He is due to appear in court on 20 April.
Despite acting swiftly, Cardiff could face further repercussions depending on Dean's report.
The Football Association of Wales has refused to comment on the incident until they have read the report.
The FAW will then have three weeks to decide if the incident merits any punishment for Cardiff City as the host club, while the Football League could also investigate.
Cardiff have been plagued with a hooligan reputation that the club have been trying to repair.
Cardiff chairman Peter Ridsdale said the club was confident that the person responsible for Dean's injury would be punished.
"We've got CCTV evidence and therefore we've now identified an individual who threw a coin, we believe it's the individual whose coin hit the referee," Ridsdale said on Sunday.
"Assuming it is the right individual... he will be banned for life from all Cardiff City matches.
"It's a disgrace, it's unacceptable, it makes you sick because obviously we spend a lot of time at Cardiff City trying to do the right thing.
"Today was always going to be a high-profile game, you don't expect idiots to do that, people like that have no place in football and certainly no place at Cardiff City."
Referee Dean was struck on the head from a missile thrown from Ninian Park's Popular Bank terrace in the 2-2 draw in Cardiff.
"It's ridiculous as I thought those days were long gone," said Jones.
"That incident was the last thing this club needs, we have worked so hard at this football club, not just in my time, to improve the reputation.
"It takes the edge of a really good game of football, why anyone would want to do that is beyond me - it is total stupidity. It is just a game of football, that's all.
"It was an absolutely crazy thing to do... throwing a coin could have easily taken someone's eye out.
Referee assault angers Ridsdale
"It could have hit one of our players, one of the Swansea players or the referee. Why do it?
"It's the last thing we need down here. We've worked really hard to get away from all that and improve our image - I can't understand the mentality of the person.
"We have all the banter, the shouting and atmosphere but it's just a football match.
"If the coin had taken someone's eye out and maimed them then whoever did it would be facing a far more serious charge.
"I hope it doesn't mar the occasion because it was a fantastic game of football that had everything in it, tension, nerves, the excitement of them scoring and thinking they've won then the last-minute penalty controversy.
"All of the players conducted themselves properly and the referee had a good game but it is sad because we're not talking about the game."
Meanwhile Cardiff City Supporters' Trust have condemned the "mindless idiots" who threw coins and said the club should not be penalised for the "actions of a tiny minority".
In 2007, Conference South side Newport County were fined £3000 by the FAW for failing to control their supporters.
Fourth official Alan Sheffield had been hit in the head by a coin thrown from the crowd in the match, also against Swansea in an FA Cup tie.
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