The proceedings relate to "the improper conduct of supporters (display of racist banners and symbols)" during Monday's Group C match against Spain in Gdansk, UEFA said Wednesday
UEFA is also investigating "the setting-off and throwing of fireworks" by Croatia fans and the "improper conduct of the team," which had six players booked during the 1-0 loss.
The new probe was opened by UEFA only a day after it fined the Croatian FA €80,000 ($101,000) for its supporters' racist abuse of Italy forward Mario Balotelli in the team's second match at Euro 2012. Stadium monitors showed 300 Croatia fans making monkey noises at Balotelli, who is black.
The association was also fined €25,000 ($31,500) last week for its fans' behavior at an earlier match against Ireland.
Croatia was eliminated from Euro 2012 after finishing third in its group.
UEFA's disciplinary body will deal with the new case on Sunday.
UEFA President Michel Platini said at a media briefing on Monday that the poor behavior of Croatian fans had soured an otherwise impressive tournament in Poland and Ukraine.
After saying he was "not happy with the Croatian people," Platini described the atmosphere at Euro 2012 stadiums as "99 percent great. The people who come to the stadiums, they were nice, except some Croatians."
Croatia's games against Ireland and Italy were both delayed to clear fireworks and smoke from the field after goals by the Croatians.
On Sunday, Croatia coach Slaven Bilic defended his country's image after UEFA announced its first racism charge against the federation.
"We are not a racist country and that's why we are so angry with these couple of crazy supporters," Bilic said.
