Riot police were called in to disperse a number of Three Lions supporters on Sunday night ahead of the game at the Benito Villamarin Stadium, home of Real Betis.
Similar scenes marred England's friendly against Netherlands in Amsterdam earlier this year and the FA has said that it will work alongside the UK Football Policing Unit to try and identify those England fans responsible for the disorder in Seville.
The statement read: "We condemn the unacceptable behaviour witnessed in Seville.
"With the Spain fixture still to come on Monday night, we urge those following the team to respect our hosts and act in a responsible manner.
"The FA will work in partnership with the UK Football Policing Unit to help identify those involved and we will sanction any England Supporters' Travel Club member found to be responsible for disorder."
England face Spain on Monday, after drawing 0-0 with Croatia over the weekend.