England's under-21 victory in Serbia was overshadowed by unsavoury scenes at the final whistle with scuffling on the pitch amid accusations of racism from the stands towards England left-back Danny Rose.
UEFA announced charges on Wednesday night against both the Serbian football federation (FSS) and the English Football Association for the improper conduct of their players, and against the Serbs for "alleged racist chanting" by fans.
The FSS has now revealed an internal investigation is also under way.
Meanwhile, the English FA has sent UEFA a full dossier of evidence, including video footage and a catalogue of incidents which they reported to match officials during and after the match, with FA general secretary Alex Horne questioning whether they will play matches in Serbia again.
Norwich boss Hughton maintains now is the time for Europe's governing body to take stern action.
"This gives UEFA a really good opportunity now to stamp their authority on this situation. It is not the first time," said Hughton, speaking ahead of Norwich's Barclays Premier League game against Arsenal at Carrow Road.
"Fortunately here in England we have done a lot of good work and have reaped the benefits from it.
"However, it seems to be a situation in Europe which seems to be rearing its ugly head on a lot of occasions.
"There is an opportunity now for them to be big and brave, to stamp down on it and I sincerely hope they do, because it deserves it.
"What we have seen over the last few years are fines which are so minimal, they are no deterrent.
"The only way for it to be a deterrent, certainly abroad, is to play games behind closed doors and ban teams.
"Fines don't work, they are paid off very quickly and they are no deterrent.
"All of us in the game want to see improvements made.
"We have made great strides here in England, and for that to happen abroad, there has to be stronger deterrents."
Hughton, 53, admits he was subjected to racist abuse during his time as a player, but feels recent initiatives such as Kick It Out and Show Racism The Red Card have made a positive impact on the domestic game.
The former Tottenham defender believes it is also the responsibility of match officials to take the appropriate action during games where racism occurs.
"There is no doubt none of us want to go through those circumstances or for our players to, but there has to be a correct way of doing it, that is from team leadership to the referee. The referee does have a responsibility to act upon what he sees and hears," Hughton said.
"There has to be correct procedure - any player that happens to has to make his captain and his manager aware of what the circumstance is.
"It is then a responsibility for the referee, and he has it within his powers to act upon that. That has to be the correct way of going about it."