Police have arrested 10 people in the Millwall end of Wembley Stadium during their team's 2-0 FA Cup semi-final defeat by Wigan Athletic.
There were scuffles in the closing stages of the game.
The Metropolitan Police said the arrests were made following "sporadic disorder".
The Football Association said it "deplored" the "unacceptable" behaviour and said "everything will be done to take action against those involved".
General secretary Alex Horne said the FA and the Met Police were investigating scenes of "violence and disorder".
"We will look to ensure those involved are identified and we would call for criminal charges and a football banning order to be brought against them," he added.
Millwall boss Kenny Jackett said he had not been aware of the violence but said the club had "worked very hard" to lose its reputation for hooliganism.
"I promise you, I wasn't aware of it during the game - I am not saying it didn't happen," he said in a post-match interview.
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