The Football Association and Metropolitan Police are continuing to search for a number of Millwall fans who caused trouble during the League One play-off final.
Barnsley's return to the Championship after their 3-1 win over the Lions on Sunday was overshadowed by trouble during and after the game.
A group of Millwall supporters attempted to break into the Barnsley end at Wembley, forcing a number of supporters to move to stay out of the way as the violence broke out and the club has vowed to hand out lifetime bans to anyone found guilty.
Fifteen arrests were made outside the ground but there have been no arrests with regards to the trouble inside Wembley.
The FA is working with members of both clubs and the Metropolitan Police to identify those who were involved in the disturbances and issued a statement surrounding the issue.
The FA condemns the disorder caused by a small number of fans at the League One play-off final between Barnsley and Millwall at Wembley Stadium.
We will work closely with the clubs, the Football League and the Metropolitan 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 have appointed Neil Harris as their permanent manager just a day after they were condemned to relegation.
Harris, the club's all-time record goalscorer, was named interim boss after Ian Holloway was sacked in March but was unable to keep the Lions in the Championship.
Steve Evans told Millwall striker Lee Gregory to "look forward to League One" after Rotherham secured their Sky Bet Championship survival and sent the Lions and Wigan down.
The Millers, deducted three points by the Football League for fielding an ineligible player, beat Reading 2-1 on Tuesday night in their game in hand to book their place in the Championship for a second season.
South-Yorkshire born Gregory had said he "(hoped) Rotherham bottle it" in their final two games of the season, which would have allowed his side the chance to stay up.
And Rotherham manager Evans was quick to remember those comments in the aftermath of his side's victory.
In a live interview with BBC Radio Sheffield shortly after full-time the Scot said: "A Millwall player said we've not got bottle. I've got 12 bottles of pink finest Champagne and we'll be drinking them for about a week.
"Look forward to League One, son, and keep your trap shut."
Millwall's hopes of Championship survival were dealt a huge blow after two late goals were enough to give Blackburn Rovers a 2-0 win.
Rudy Gestede's sumptuous volley in the 78th minute finally broke the deadlock for Rovers and substitute Jordan Rhodes settled it in injury time, catching an increasingly desperate Millwall side on the break.
Millwall grabbed at their possible relegation lifeline by beating Wigan 2-0 in a dramatic win-or-bust encounter.
Goals from Jimmy Abdou and Magaye Gueye settled a bad-tempered clash which looks certain to spell the end of Wigan's stay in the Sky Bet Championship.
Both sides learned on Monday that Rotherham, the team directly above them just outside the drop zone, could face a three-point penalty for fielding an ineligible player.
Championship side Millwall have sacked manager Ian Holloway with immediate effect.
Lions chairman John Berylson told the club's official website: "This was a hard decision to take because we very much hoped that Ollie would prove to be the man to take us forward and on to the next level. I would like to thank him for his efforts, and in particular for keeping us in the Championship last May.
"This season, though, has proved to be an extremely challenging one and we now find ourselves facing another uphill battle to avoid relegation.
"Ian Holloway remains a fine manager and it was his impressive track record which led us to appoint him some 14 months ago. However, our view is that the decision to part company at this stage is in the best interests of the football club going forward.
"Neil Harris has agreed to take over managerial duties for the remainder of the season and I am confident that Millwall fans will give him every support over the next couple of months as we strive to turn our current run of form around."
Championship side Rotherham have condemned the violence of Millwall fans during the club's game at the weekend.Read the full story ›
Rotherham staged an impressive second-half comeback to win 2-1 and boost their Sky Bet Championship survival hopes while damaging Millwall's chances of staying in the division.
The Millers, who trailed to Martyn Woolford's early opener, recovered after the break and hit back through goals from Danny Ward and Kari Arnason.
Ward struck after just 73 seconds of the second period while Arnason headed home from a corner five minutes from time.
Bradford City and Millwall have been charged by the Football Association for failing to ensure their players conducted themselves in an orderly fashion and/or refrained from provocative behaviour.
The charge refers to an incident in the 28th minute of last week's FA Cup third round replay, which Bradford won 4-0 to set up a fourth round meeting with Chelsea.
Bradford manager Phil Parkinson and assistant Steve Parkin have also been charged for improper conduct.
All parties have been given until 6pm on January 21st 2015 to respond to the charges.
Millwall chairman John Berylson has promised to refund every one of the 456 Lions fans who travelled to the humiliating FA Cup loss at Bradford.
The Millwall boss, Ian Holloway, apologised to the supporters after his side was thumped 4-0 at Valley Parade.
A statement on the Millwall website read:
Following Wednesday night's FA Cup Third Round replay defeat to Bradford City, Millwall chairman John Berylson has decided to refund the cost of match tickets for the 456 Lions fans who purchased their tickets in advance of the game.
He wishes to thank everyone for their continued support during difficult times and has pledged to facilitate further squad strengthening with a view to seeing results improve in the very near future.
An announcement detailing the refund process will be released in due course.