Cologne have received four separate UEFA charges after fans caused disturbance at the Emirates which resulted in the match being delayed by an hour.
However, the German side have deflected blame from themselves onto Arsenal and the police, accusing them of being ill prepared for the Europa League clash.
Though Arsenal have escaped major sanction for their role in the chaos, expecting a fine of less than £10,000, Cologne have seen charges related to missiles thrown, fireworks, crowd disturbances and acts of damage.
The Bundesliga outfit released a statement apologising for the behaviour of some fans, saying there was "no excuse" for attacks on police and Emirates Stadium staff, but also claimed that Arsenal and the Met Police were "unfortunately, not adequately prepared for the task".
"In our view, the security concept and communication seemed inadequate and the police force too small," said the German club.
"Due to the enormous demand for tickets, it would have been sensible, not least for security reasons, to allow more than the allocated five per cent of stadium capacity to the guest [away] fans.
"It was apparent that thousands of people from Cologne would seek to avoid the restrictions and get tickets in every way possible.
"One such way would be through the help of Arsenal supporters, who passed on their tickets to the FC [Cologne] fans. Some as gifts, but some also for horrendous prices."
It was the German side's first European match for 25 years, though it would ultimately end in a 3-1 defeat to the 'Gunners'.