England fans sang anti-Islamic songs while in Prague supporting Thomas Tuchel's side against the Czech Republic.
Footage has emerged of supporters in a bar in the Czech capital singing "Allah, Allah, who the f--- is Allah?" to the tune of Smokie's 1972 song Living Next Door To Alice .
A Football Association spokesman said: "We will not tolerate this unacceptable and deeply offensive chanting, and will work with the UK police who attend all England home and away matches to identify the perpetrators and take the necessary action "
Anthony Gordon and Harry Kane scored in the 2-0 Nations League win at Fortuna Arena. England were given a ticket allocation of 1,000 for the second match in Group A3.
Before the match in Prague, governing body Uefa posted an anti-discrimination video along with warnings in the stadium.
"Discrimination of any kind has no place in football," Uefa said in the video. "This game is for everyone, regardless of background, gender, or ability."
It was England's first match abroad since the World Cup in the summer, when Tuchel's side reached the semi-finals in North America.
Djed Spence became the first Muslim player to represent England last year after making his debut against Serbia in a World Cup qualifier.

Djed Spence became the first Muslim player to represent England last year - Getty Images/Eston Parker
England play Croatia in Rijeka on Saturday, although there will barely be any fans attending the game.
Croatia were punished for crowd trouble by playing matches behind closed doors, but 100 England fans will be allowed to watch the game at Stadion HNK Rijeka. The extended international break then wraps up with the return game against Czechs on Tuesday.

