Croatia boss Ante Cacic has called the supporters who threw flares on to the pitch in their Euro 2016 draw with the Czech Republic "sports terrorists".
The match, which ended 2-2, was halted in the 86th minute when flares from the Croatia end rained down on the Saint-Etienne pitch.
Uefa has confirmed it will investigate the incident.
"They are not really Croatia supporters. These people are scary and I call them hooligans," said Cacic.
Croatia has already been charged by Uefa after crowd trouble in their opening Group D game against Turkey.
Uefa said disciplinary proceedings would be opened on Saturday once they had received the official reports about the trouble from the match delegate and English referee Mark Clattenburg.
Cacic also hopes the Croatian FA will take action, adding: "The 95% of Croatian supporters are ashamed in front of Europe.
"These are sports terrorists. 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."
Uefa is also expected to open disciplinary proceedings against the Turkish FA after some of the country's fans set off flares at the end of their 3-0 defeat by Spain in Nice.
Before that game, three Spanish "ultras" fans were arrested for trying to bring flares into the stadium, while another three were arrested for carrying neo-Nazi banners.
A steward escaped serious injury when one of the flares thrown from the stands exploded
Croatia was winning 2-1 when trouble broke out, with a number of flares thrown onto the corner of the pitch, while some Croatia fans began fighting among themselves.
Journalist Andy Mitten, who was at the game, told BBC Radio 5 live: "I was in a section full of Croatia fans. The team was playing really well, everything was good, the people around me were happy but then I noticed a big line of police and soldiers building up in front of the Croatia end.
"It became clear they knew something was going to happen and it did happen. I saw fighting. It was horrible to watch."
The Croatian players appealed to their fans to calm down, and after several minutes, play was finally able to resume.
However, with Cacic's side seemingly affected by the events, the Czech Republic equalised in the 93rd minute through Tomas Necid's penalty after a handball.
"We have to say sorry to Uefa, sorry to the Czech Republic and to everyone around the world who loves football," said Croatia midfielder Ivan Rakitic.
"Most supporters support this team and are real supporters. But 10 individuals can make all these problems. It is clear that the Croatian FA and [Croatian FA president] Davor Suker are fighting against this.
"I hope Uefa can understand this."
Croatia was sanctioned by Fifa last month because of "discriminatory chants by fans" during friendlies with Israel and Hungary in March, meaning they will play their next two 2018 World Cup qualifiers behind closed doors.
Former Croatia boss Slaven Bilic condemned the scenes but warned there will be more crowd trouble.
The West Ham manager suggested some fans had only travelled to the tournament from Croatia to cause trouble.
"It's unbelievable what those people are doing," Bilic told ITV. "Some of them are there on a mission. It's probably not the last time they'll do it," he said.
"Back home it's not the greatest league, but it's competitive. When there's a big derby between Dinamo Zagreb and Hajduk Split people are not taking their kids because they know it'll be dangerous."