The Three Lions were jeered for taking a knee before the start of the game, pelted with plastic cups after goals and players of colour were harassed.
Football's world governing body announced on Friday that it has opened disciplinary proceedings over the racist abuse of England players during a World Cup qualifier match against Hungary the previous evening.
"Following analysis of the match reports, FIFA has opened disciplinary proceedings concerning the incidents last night at the game Hungary-England," the body said in a statement.
"Once again, FIFA would like to state that our position remains firm and resolute in rejecting any form of racism and violence as well as any other form of discrimination or abuse. We have a very clear zero-tolerance stance against such abhorrent behaviour in football," it added.
The announcement comes hours after British Prime Minister Boris Johnson called for "strong action" from FIFA, describing the racist abuse directed at England players as "completely unacceptable".
"I urge FIFA to take strong action against those responsible to ensure that this kind of disgraceful behaviour is eradicated from the game for good," he added.
The Three Lions were jeered for taking a knee before the start of the game — a gesture denouncing racism — and were pelted with plastic cups after goals. Players of colour were also reportedly harassed with monkey noises throughout the match.
England manager Gareth Southgate said after the clash — which ended in a 4-0 victory for England — that his players, including 18-year-old Jude Bellingham, "should not have to endure this suffering".
He added that he had not personally seen the racist abuse and that he did not believe that all Hungarian fans were involved — but that those who were should not be excused. Garreth was pelted with ice during his interview.
England's Football Association described it as "extremely disappointing to hear reports of discriminatory actions towards some of our England players."
"We will be asking FIFA to investigate the matter," It added.
The Hungarian Football Association (MLSZ) said on Friday that "the vast majority of the 60,000 fans visiting the Puskas Arena were sporting, encouraging the Hungarian national team, even when the team was already losing."
"It is in their defense that the disruptors need to be identified and severely punished."
"Fans entering the field, throwing light grenades and glasses, are being identified. The MLSZ has filed/will file a police report against them. Any fine will be passed on to the perpetrators in civil litigation, and they can expect a two-year disqualification from sporting events at the end of the trial," it added in a statement.
Marco Rossi, who manages the Hungarian national team, had urged supporters not to behave that way before the match.
Hungary had been ordered to play its next two matches in front of an empty stadium by the UEFA — Europe's governing body for football — following this summer's Euro championships because of racist and homophobic abuse observed during games held in Budapest.
But supporters were allowed in the stands on Thursday evening because the European qualifying matches for next year's World Cup in Qatar, fall under FIFA's jurisdiction and not the UEFA's.
Hungarian Foreign Minister Péter Szijjártó seemingly dismissed accusations lobbed at his country's supporters on Friday morning, sharing a video in a Facebook post and writing: "English players complain about the "hostile atmosphere in Budapest yesterday". The following footage was taken at Wembley before the European Championship final. The Italian national anthem can barely be heard amidst the whistling of the England fans. Did they make similar statements then?"
Several black members of the England squad were subjected to serious online racist abuse by British fans following the Euro final, after missing their penalties which resulted in an Italian victory.