The Croatian and English Football Associations were charged by UEFA, European football's governing body, for improper behaviour at their Euro 2008 qualifier in Zagreb on October 11.
The charges relate to incidents inside and outside Dinamo Zagreb's Maksimir Stadium where Croatia beat England 2-0 in their Group E qualifier.
The charges will be heard by UEFA's Control and Disciplinary Body at UEFA's headquarters in Nyon, Switzerland, on November 9.
William Gaillard, FIFA's Director of Communications told Sky Sports News: "The charge against the Croatian FA is that they mis-handled the entrance procedure and there was crowd misbehaviour."
He said the charge against the English FA related to fans' behaviour.
Adrian Bevington, spokesman for the English FA, told Sky Sports News: "We are extremely surprised to have been charged by UEFA. We will contest this and request a personal hearing and seek to call up as many witnesses as we require.
"We have had a vast amount of communication and correspondence from English supporters who were in Zagreb who faced difficult situations during the game."
Bevington said the English FA were not responsible for policing outside the stadium where a major incident was caused when a number of turnstiles were suddenly closed without warning as fans were entering the stadium creating a serious bottleneck.
FANS ARRESTED
The Croatian FA said they had received a request from UEFA to provide information on several flares that were lit up and problems that occurred at the entrance to the stadium.
"We will soon respond to UEFA's questions," FA's Secretary-General Zorislav Srebric told Reuters.
Croatia is bidding with Hungary to co-host the Euro 2012 Championship and any crowd trouble involving local fans or stadiums may cast a cloud over the bid.
"It's true that such events do not go in favour of our bid, but I don't believe they will seriously put it under jeopardy," Srebric said.
Croatian police detained more than 200 supporters for disorderly behaviour surrounding the match.
A police statement said that 187 Croatian fans and 31 English supporters were detained for incidents away from the ground while a further 25 England fans were arrested inside the stadium shortly after the match kicked off following a clash with stewards at one of the gates.
The police report said that England fans assaulted security staff at the entrance to the southern tier, after which 25 of them were detained.
Police said 20 visiting fans were released immediately after the match.
(Additional reporting by Igor Ilic in Zagreb)