Life bans expected for Upton Park aggressors
"We absolutely condemn all of the disorder that has occurred at Upton Park... both inside and outside of the ground," an FA statement read.
Fans clashed outside the Premier League club's Upton Park stadium before kick-off and supporters invaded the pitch twice after West Ham scored in extra-time to beat the third division side 3-1.
A 44-year-old man was taken to hospital with a stab wound.
"We will very quickly be working with all parties, including the police and clubs to establish the facts," the FA statement continued.
"We expect all culprits to be banned from football for life - they have no place in our game."
West Ham said they would investigate fully the "deplorable" scenes.
"The club will not tolerate the unacceptable behaviour witnessed... and will take the strongest possible action against anyone found responsible, including life bans."