Almost 80 fans were arrested as violence spread from stadiums to the streets and transport network, prompting fears that the "English disease" had resurfaced.
"You never finally defeat football hooliganism," British sports minister Hugh Robertson told The Associated Press. "Huge, huge strides have been made since the 1980s. The situation has been transformed but we don't appear to be able to make it go away forever.
"You've got to remain vigilant and remain tough when it occurs."
Police are acting quickly to prevent the disorder spreading as the season enters its final month.
"It is too soon to say if this is an emerging trend," said Andy Holt, who oversees policing of football in England at the Association of Chief Police Officers. "But we will review what happened at the weekend and make any changes if they are necessary."
Wembley witnessed its most violent scenes since the rebuilt national stadium opened six years ago as Millwall fans turned on each other during Saturday's FA Cup semifinal loss to Wigan.
Fourteen arrests were made inside the stadium as the disorder was allowed to build throughout the second half in the Millwall end. As trouble spilled out of the stadium into a nearby tube station, another six Millwall fans were arrested for a series of offenses, including affray and racist abuse.
Fans of the second-tier London club, which was renowned for its struggle with hooliganism in the 1970s and 80s, made light of their unruly reputation by chanting: "No one likes us and we don't care."
But the American-owned club has sent out a clear message that it does.
"The reputation of our club, which over the last few years has been steadily and painstakingly rebuilt, has been severely damaged once again," Millwall chief executive Andy Ambler said after talks with Football Association chiefs on Monday. "We understand that there are now bridges to be rebuilt, and if there are lessons to be learned from the weekend I'm sure all parties will be keen to take them on board and ensure that those unsavory scenes are not repeated."
Ambler vowed to help bring the perpetrators of the "mindless violence" to justice, and Newcastle was also forced to condemn its own fans on Monday.
Newcastle fans responded to a 3-0 loss at home to local rival Sunderland on Sunday by running amok in the city center, with three police officers injured after being attacked during clashes.
In one scene that provoked widespread outrage, a man was also seen swinging at a police horse. Thirty men were arrested, and Newcastle vowed to impose lifetime bans from matches on anyone found guilty.
"We were embarrassed and appalled by the behavior of a minority of so-called fans who last night were involved in disturbances and disorder," Newcastle said in a statement.
British Transport Police also reported unrest on Sunday with fans traveling to and from the FA Cup semifinal between Manchester City and Chelsea. Seven Chelsea fans were arrested and four City fans were held for offenses including assault and racist abuse.
On Saturday, 11 fans of second-tier club Watford were also arrested as they traveled from a match at Peterborough through London's King's Cross rail station
"In recent years, police, football clubs and other partners have made great strides in tackling the (hooligan) problem, and we've seen enormous reductions in offenses thanks to a combination of robust policing and the banning of troublesome individuals from attending matches," said Andrew Trotter, chief constable of the British Transport Police.
"The scenes at Wembley Stadium on Saturday and in Newcastle on Sunday serve as a firm and sobering reminder that there is still much more to be done in tackling football-related disorder."
The incidents came days after the 2018 World Cup organizing committee said they are looking to England to see how to solve Russia's own hooliganism annulled.
"What you achieved in England in the past 30 years was a true revolution," World Cup director Alexander Djordjadze said.
But the ugly reminder over the weekend of England's hooligan past has reinforced the urgency to make sure the progress in cleaning up the game isn't lost.
"The events of the weekend ... do not represent a return to the dark days of the 70s and 80s," said Robertson, the government minister with responsibility for football. "The world saw the very best of British sport last summer (at the London Olympics). The last thing we want is these sorts of incidents."
Robertson said the early indications are that the incidents were caused by a "combination of too much drink, warm weather and an enormous amount of stupidity from the fans involved."
Worse crowd disorder has been witnessed on the continent this season, with three Borussia Moenchengladbach fans stabbed in Rome ahead of a Europa League match against Lazio in February.
A Tottenham supporter was also stabbed in Rome in November, while the London club's fans were attacked in a Lyon pub for another Europa League game in February.
This weekend saw riot police deploy tear gas in Italy to deal with disorder outside AC Milan's match against Napoli.
And in Brazil, two Ceara fans were shot in the head after being confronted by supporters of local rival Fortaleza while traveling to a stadium being used at the 2014 World Cup.