Croatian fans hurled flares on to the pitch in Saint Etienne in the 86th minute of the 2-2 draw with Czech Republic on Friday, while Turkish fans let off flares after their 3-0 defeat by Spain in Nice.
UEFA said Croatia was accused of crowd disturbances, racist behaviour, setting off fireworks and throwing objects.
Croatian coach Ante Cacic called the country's fans "sports terrorists" after the incidents which caused a four-minute halt to the match.
UEFA has accused Turkey of a pitch invasion, throwing objects and setting off fireworks.
Related news:
> French government backs police after Euro 2016 fan violence
> Russians jailed for Euro 2016 violence, far-right figure expelled