Football Association chief executive Brian Barwick claims weekend incidents of coin throwing are 'absolutely unacceptable' and has urged supporters to help catch the culprits.
The first round of the FA Cup was marred by controversy at non-league clubs Newport and Barrow on Saturday, when missiles were thrown from crowds.
Fourth official Alan Sheffield needed medical treatment for a head wound when he was struck by a coin in County's all-Welsh tie with Swansea and the FA of Wales are set to investigate.
Meanwhile, it emerged today that Bristol Rovers goalkeeper Steve Phillips was also targeted by a supporter during the match at Barrow.
The coin missed on that occasion but Cumbria Police have launched an appeal for witnesses in a bid to catch the fan.
There have been similar incidents at Premiership matches, with Fulham's Claus Jensen hit by a coin against Everton and Arsenal's Robin van Persie struck during the game at West Ham.
And Barwick has prescribed strong punishments for the guilty parties if they are identified.
'While it's important to remember that the overwhelming majority of this weekend's games showed the positive nature of the Cup, there were unfortunately a couple of examples of missile-throwing which have marred a number of games recently,' he told the FA.
'The incident at Newport will be investigated by the FA of Wales while we will continue to make inquiries into the other recent incidents.
'It is absolutely unacceptable for players' or match officials' safety to be threatened during a match.
'We are urging clubs to do everything they can in conjunction with the police to identify the culprits.
'We want those people banned from attending matches. This is a recent trend which has to stop now.'
Barwick continued: 'It is vital for fans to play their part in identifying these people who are committing criminal offences.
'We should not let a small number of idiots ruin the reputation of clubs and their true fans, and also ruin the spectacle of attending live football.
'I'm asking fans who witness fans throwing missiles to alert the authorities within the stadium - we need your help on this one.'
FAW secretary David Collins said the incident at Newport could result in both the club and some officials being punished.
'The FAW is investigating the events which occurred and once we have received all the evidence we will then take a decision with regard to misconduct charges against Newport and officials associated with the club,' he told Sky Sports News.
'Under the law a ban could naturally follow.
'All aspects of the incident will be investigated. We have received the referee's report, we are awaiting film of the incident as well as a report from the police.
'Once all that has been gathered we should be able to make a decision pretty quickly, probably later this week.'
Police are examining TV footage of the game at Newport.
Gwent detectives are scrutinising TV footage of the match together with video recordings taken by their own officers.
Detective Inspector Steve Webber said: 'I now have a team of officers looking at this particular incident and we are liaising closely with the club in an effort to trace the offenders.'