Millwall's 2-0 FA Cup semi-final loss to Wigan was marred after ten of their own supporters were arrested for fighting among themselves and with the police while the game was still in play.
Police were called into action and forced to use batons to control the violence, while television footage showed young Lions supporters crying and one man with blood pouring from his face.
A number of Millwall fans booed those causing the trouble and missiles rained down on the lower tier of the Championship club's enclosure from those sitting above.
A Scotland Yard spokesman said: "Ten people have been arrested following sporadic disorder among fans in the Millwall supporters' area at Wembley. Investigations into the circumstances of the incidents are continuing.''
The fighting had been going on for at least two minutes before officers and stewards arrived, and questions are now likely to be asked over the policing and stewarding of the Wembley clash.
The Football Association released a statement condemning the violence and have also launched an investigation.
Alex Horne, general secretary of the FA, said: "The Metropolitan Police and The FA are this evening investigating scenes of sporadic violence and disorder in the Millwall FC end at today's FA Cup Semi-Final. The FA and Wembley Stadium will work with police and representatives of Millwall FC to review all events. 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. The FA deplore the scenes which have taken place, which are unnacceptable. Everything will be done to take action against those involved."
Chairman John Berylson, who flew in from the United States for the game, added: "There are always a few idiots. That's not our fan base and we don't even know who those people are. We will be investigating.''
Lions manager Kenny Jackett was not aware of the violence when questioned on the matter after the full-time whistle.
"I've just heard about that,'' he said. "I wasn't aware of any fighting during the game, not aware of any problems. I'll need to examine the facts before I can give an opinion. I promise you, I wasn't aware of it during the game. I am not saying it didn't happen. Until I see it, it is difficult to form an opinion. We want to be talking about football. I need to be able to form my own opinion. I am sure the evidence is there. I am not denying that.''
The London club have a history of being troubled by hooliganism and have been working hard over the past few years to improve their image within the game.
And Jackett has vowed Millwall will continue to do all they can to rid themselves of their reputation.
"That has been our greatest challenge,'' he said. "We want to try and work hard to keep momentum going forward. I understand what you are saying. If there was crowd trouble... It will hold us back if that happens repeatedly. We have worked very hard, the chief executive and chairman, to do everything we possibly can to be trouble-free. We have had high-profile games that have gone very well. We have done everything we possibly can.''
After being told some children were carried out crying, he said: "I am very sorry if that is the case. Until I see those images, for me to comment is a tough one.''
Millwall captain Danny Shittu added: "Today was meant to be a good day out at Wembley. I'm disappointed by it. It's sad to hear about these things happening on a day like today. Things like that shouldn't be going on, it should be a great day for both sides.''
Wigan manager Roberto Martinez, whose team will face Manchester City or Chelsea in the final next month, spoke of his disappointment on hearing of the violence.
He said: "It's a real shame because the game on the pitch was a great advert for the competition. A small minority give the game a bad name.''
Wigan chairman Dave Whelan added: "I can't understand why the Millwall fans would fight each other. I understand if they want to fall out with the visiting team, but why would they fall out amongst themselves? It just gives football a very, very poor reputation. We know Millwall are a tough club, their team's tough to play, the supporters are Millwall, Millwall, Millwall straight through. But don't fight each other. I couldn't understand that.''
Information from the Press Association was used in this report