Flares were thrown on the pitch and fighting broke out in the Croatian end during their 2-2 Group D draw with the Czech Republic - leaving them likely to face UEFA sanctions.
Referee Mark Clattenburg was forced to stop the game with four minutes left while a steward was almost hit by a firecrakcer, along with Croatia goalscorer Ivan Perisic.
It forced 10 minutes of stoppage time, allowing Tomas Necid to score a late penalty and snatch an unlikely draw after the Czech Republic were outplayed for 75 minutes.
The violence was condemned on Twitter.
Many wondered if security should have done more.
Croatia boss Ante Cacic told a press conference: "These people are really scary, that is why I call them hooligans. These are not really Croatian supporters. These are sports terrorists. The main thing our country doesn't want to mess with, this kind of hooligans.
"This is maybe just a question about six to 10 individuals. I hope they can be identified and punished. I hope the Croatia FA is doing everything to prevent this but it is impossible to avoid."
He added: "Ninety-five percent of our supporters are ashamed in front of Europe, the players are very sad that after playing a beautiful match this happens."