Some Millwall fans could face life bans after they forced Barnsley supporters to flee to safety as they tried to break into the opposing team's end at Wembley.
The south-east London club made the threat after the ugly scenes which marred Barnsley's 3-1 win over Millwall in the League One play-off final on Sunday.
Fans had charged around the top tier attempting to force their way into the opposing end while others appeared to lob coins at Tykes players.
The FA, English football's governing body, said it "condemns the disorder caused by a small number of fans" at the match.
A spokesman said: "We will work closely with the clubs, the Football League and the Met Police to identify those involved and take appropriate action. "We would like to take this opportunity to praise the actions of our stewards and the police, who responded responsibly under provocation ."
Millwall fans had previously fought amongst themselves during the 2013 FA Cup semi-final against Wigan at Wembley.
Metropolitan Police said 15 arrests had been made outside the ground. Enquiries are continuing into matters inside the stadium but no arrests have been made so far.