Crowd problems began in the Hungarian section of the crowd within three minutes of kick-off at Wembley – as a fan was arrested for racist abuse.
Hundreds of Hungarian supporters formed a line for the managers working in the small arena closed to the visiting fans.
In horrific scenes, groups of stewards, numbering about 20, were left to fend for themselves under attack from all angles as tensions spread.
They received welcome reinforcements from the police, who tried to break in with batons in an attempt to restore order.
But the stewards and the police line were chased down as they were punched and kicked through the tunnel under the stand.
On the strength of the attack, a policeman broke his leg and had to be taken out safely.
The game continued as normal as England attacked the left wing from where there was trouble.
Riot police and stewards finally restored order under the stand, as anger began to subside.
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The Metropolitan Police confirmed at half-time that there had been an arrest on charges of racist abuse by an unidentified supporter – adding to the crowd’s woes.
The tweet read: “Shortly after the start of tonight’s match at Wembley, officials to arrest a spectator for a racially aggravated public order offense following comments made toward a steward entered the stand.
“As officers made the arrests, minor chaos ensued involving other onlookers.
“Order was quickly restored and there have been no further incidents at this stage.”
An FA statement said: “We are aware of an incident in the away class during tonight’s FIFA 2022 World Cup qualifiers at Wembley Stadium.
“We will investigate and report the incident to FIFA.”
After storming the turnstiles at the Euro 2020 final in July, Wembley has had trouble for the second time this year.
The FA is still awaiting UEFA’s disciplinary decision on that incident – and the governing body is certain to investigate this latest violence.
The FA was expecting around 1,000 visiting supporters for the World Cup qualifiers, most of whom were based in the UK.
Hungarian fans booed before kick-off as England players knelt while the visiting team stood.
A banner was hoisted showing a symbol against kneeling – but the home support responded with loud applause.
Later, after further trouble, the riot police took a stand under the stand under the Small Away section.
Wembley’s match was a comeback from last month’s match at Puskas Arena in which racist abuse was aimed at England players.
Three Lions players were also pelted with objects in the second half and a fiery throw was made on the pitch by home fans, prompting FIFA to initiate disciplinary proceedings after the game.
Despite UEFA ordering Hungary to play three home games behind closed doors after discriminatory treatment of its supporters at Euro 2020, fans were allowed to come under FIFA’s jurisdiction.
England described the abuse as ‘totally unacceptable’, while British Prime Minister Boris Johnson urged FIFA to take ‘strong action against those responsible for the abusive behaviour’.