London - European football chiefs charged Arsenal and Cologne on Friday after vast numbers of away fans gained access to the home sections of Emirates Stadium, sparking chaotic scenes that marred the Europa League clash.
Visiting supporters were issued with 3 000 tickets but around 20 000 fans of the German club are believed to have made the journey to the British capital.
The start of Thursday's Group H match was delayed by around an hour as ticketless Cologne fans tried to gain entry to the ground in north London and there were clearly thousands of away supporters sitting among Arsenal fans, causing a security risk.
The Metropolitan Police said five people had been arrested on suspicion of public order offences and three officers had been injured as a result of the disorder, none of seriously.
Cologne said in a statement that the trouble had occurred because its supporters had been given an insufficient number of tickets while Arsenal said they would launch a "full review" of what happened.
Both clubs now face disciplinary proceedings from governing body UEFA.
Cologne fans are accused of crowd disturbances, setting off fireworks, throwing objects and causing acts of damage, while Arsenal face a probe for "stairways blocked in away supporters sector".
UEFA said it would deal with the cases on September 21.
The German club, in its statement, said: "Too few places were attributed to FC Cologne supporters because five percent of the total capacity of the stadium was not sufficient. It was predictable that several thousand supporters would try to get into the stadium by any means possible."
Cologne also criticised security arrangements at the Emirates.
"Despite the immense experience of the London security staff, who are used to Arsenal's regular European matches, those in charge did not sufficiently prepare for the event.
"The entire security plan and the communication around it appeared to us to be insufficient and there were not enough police on duty."
Earlier, YouTube footage showed thousands of Cologne fans surging through the streets of London, chanting and setting off flares.
Arsenal said they would launch a "full review into the circumstances surrounding the game and will ensure any lessons that can be learned are used in the future".
Manager Arsene Wenger was surprised the game went ahead.
"I thought they would not play the game, because I can't see the police taking any risk," he said.
"We live in a society of 100 percent security and I thought they would never take a gamble to play this game when I saw the images around the stadium. But I must say our supporters as well dealt well with the situation and there was no aggravation."
Cologne goalkeeper Timo Horn said fans who misbehaved had "brought shame on the club" and club legend Bodo Illgner, a World Cup-winning goalkeeper with Germany in 1990, also criticised the small minority of fans who misbehaved.
Arsenal's statement also said it was "very disappointing" that so many home tickets appeared to have been purchased by Cologne supporters via ticket touts after the club worked closely with police, who deployed extra numbers once the trouble began, and UEFA.
"The 3 000 tickets issued to Cologne fans was in line with competition rules but it is clear many more visiting fans arrived, causing significant congestion and disturbance outside the stadium before kick-off," it said.
"Many tickets were sold through touts and this is very disappointing and something we continue to work hard to address."
Arsenal won the match 3-1 after falling behind to a long-range strike from Jhon Cordoba before bouncing back in the second half. Substitute Sead Kolasinac equalised before goals from Alexis Sanchez and Hector Bellerin gave the Londoners the win.
Cologne coach Peter Stoeger refused to be questioned on the actions of the club's supporters, saying: "I have no comment about the fans."
"I'm the coach, my job is the team, my job is football not the fans," the Austrian added.