The Hammers have been hit with five different charges and face the prospect of a large fine and the possibility of having to play games behind closed doors.
The statement reads:
"We are reviewing the FA charges and will respond accordingly. In advance of the Millwall match, the club followed the strict advice of the police and relevant authorities at every stage of the planning process.
"That full cooperation continued on the night with the club working closely with police on a carefully set-out plan that was initiated and approved by the independent safety advisory group.
"We do acknowledge the appalling behaviour of a minority of fans inside the stadium and, in conjunction with the police, will continue to take strong and appropriate action against anyone found responsible."