Instead of being issued with cautions or fixed penalty notices for crimes such as breaking windows or using threatening behaviour, the zero tolerance approach will see misbehaving fans taken to court and given football banning orders.
The orders mean they have to surrender their passports when England are playing abroad, and cannot travel.
Nick Hawkins, a Chief Crown Prosecutor from Hampshire, who has led previous crackdowns on hooligans, said fixed penalty notices were "not appropriate" for dealing with the hooligan problem.
He said: "We know from intelligence that some of the hard-core element refer to these (fixed penalty notices) as pay-as-you-go hooliganism, so it's clearly not having the desired effect."
Police issue around 500 cautions and more than 50 fixed penalty notices for low level thuggery each season but the vast majority of those offenders will now get banning orders.
The current number of fans subject to orders is 3,067.
However, orders against around 600 hooligans are set to lapse before the World Cup Finals and there will be nothing to prevent them travelling to Germany.
In addition, 900 suspected troublemakers who are not subject to orders are being looked at by 29 special police teams across the country to see if they can be prosecuted for minor offences.
The Football Supporters Federation fears some genuine fans may be unfairly punished.
But Mr Hawkins said: "We are not talking about people celebrating and having a beer and singing, we are talking about people who do that and then decide to smash the bar up."
Chief Superintendent John Campbell, who has also been involved in hooligan crackdowns, said: "When people are given a caution or a fixed penalty in a police station they can't get a banning order because the police don't have the power to impose it."
The new policy will see a presumption that even the most minor of football-related crimes, whether in or away from a ground, will be prosecuted in court.
Cautions and fixed penalty notices will only be issued in exceptional cases and the new approach will apply across all 42 police forces in England and Wales after being agreed between the Crown Prosecution Service and senior police commanders.
Mr Hawkins said: "We are going to show football hooligans the red card.
"Hooligans hate and fear football banning orders, so the orders are a key weapon against them."
He said most hooliganism takes place away from football grounds, often around local pubs and railway or bus stations, and those offenders would be prosecuted.
David Blundell, Chief Crown Prosecutor for the West Midlands, said: "We want to prevent the small minority of yobs from travelling to Germany. The England team, the England supporters and all the other nationalities that flock to Germany will be better off without them."
David Swift, Deputy Chief Constable of Staffordshire Police, who leads anti-hooliganism efforts by the Association of Chief Police Officers, said: "There are currently 900 individuals who are being targeted by 29 dedicated policing operations across the country.
"Those officers will be seeking direction from the Crown Prosecution Service on the evidence they have collected and the positive approach to prosecution should increase convictions and bans.
"Most importantly it will help reduce the likelihood of violence by the English in Germany."Reuse content