Charges have been brought for the setting off of fireworks, the throwing of objects, crowd disturbance and racist behaviour by Croatia fans.
European football's governing body has also charged Turkey following incidents during their match against Spain.
Its control, ethics and disciplinary body will rule on the cases on Monday.
Friday's match between Croatia and the Czech Republic was halted by referee Mark Clattenburg in the 86th minute when flares were thrown on to the pitch from the Croatia end.
When the game resumed, Croatia conceded a late penalty to draw 2-2.
After the game, Croatia boss Ante Cacic called the supporters who threw flares on to the pitch "sports terrorists".
He added: "They are not really Croatia supporters. These people are scary and I call them hooligans."
The Turkish Football Federation, meanwhile, has been charged with the setting off of fireworks, throwing of objects and field invasion after some of their fans caused trouble during Friday's 3-0 defeat by Spain.
Both the Croatian and Turkish federations already face charges in the aftermath of the match between the two sides on 12 June.
Russia were given a suspended disqualification and fined 150,000 euros (£119,000) after violent scenes at the game against England on 11 June.