Arsenal will conduct a full review to determine how vast numbers of Cologne supporters gained access to the home sections of the Emirates Stadium for Thursday night's Europa League clash.
The Group H opener, in which Arsenal eventually ran out as 3-1 winners, was delayed by an hour as ticketless Cologne fans looked to gain entry to the ground.
The visitors were issued with 3,000 tickets but around 20,000 Cologne fans are believed to have made the journey to London.
There were clearly thousands of away supporters sitting among Arsenal fans, causing a security risk.
Five arrests were made over the course of the evening and Arsenal issued a statement on Friday insisting the safety of supporters was the main concern at the time.
"Following last night's UEFA Europa League match with Cologne we would like to stress that fan safety was always our paramount concern and informed all decisions made," it read.
"We have launched a full review into the circumstances surrounding the game and will ensure any lessons that can be learned are used in the future."
A UEFA probe into the evening's events is a near certainty as pictures have emerged of a minority of Cologne supporters causing problems for stewards inside the stadium.
The issues only intensified when Jhon Corboda gave the Bundesliga side a ninth-minute lead with his 40-yard strike.
Arsenal came from behind after the interval as goals from Sead Kolasinac, Alexis Sanchez and Hector Bellerin secured the three points.
After the game, Cologne coach Peter Stoger refused to take questions on the crowd disturbances - but Arsenal boss Arsene Wenger admitted he thought the contest would be postponed.
Asked if UEFA should take action, Wenger replied: "They are the only master to analyse the facts of what happened. They will certainly make an inquiry to see what happened, for sure.
"They (Cologne fans) were very clever.
"I don't know how they managed to infiltrate our fans and get everywhere but they did that very well. I don't know if they went through Arsenal membership, on the internet. they did very well.
"I thought they would not play the game, because I can't see the police taking any risk.
"We live in a society of 100 per cent 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 as well and there was no aggravation."
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 working closely with the Metropolitan Police, who deployed extra numbers once trouble began, and UEFA.
"We worked in full consultation with police and UEFA officials on the night and in advance of the game and had taken extensive steps in advance to prevent tickets being sold to visiting supporters," it read.
"This included a number of measures including ensuring no tickets were sold via general sale and that no red memberships purchased after the draw were able to be used to get tickets in the home end for this match.
"We also worked with our colleagues at Cologne to stop supporters travelling without match tickets.
"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.
"Many tickets were sold through touts and this is very disappointing and something we continue to work hard to address."