England's players were booed as they took the knee prior to their World Cup qualifier against Hungary in Budapest.
The Three Lions have regularly performed the gesture before matches in a show of solidarity against racism.
But fans inside the Ferenc Puskas Stadium jeered Gareth Southgate's team as they knelt just before kick-off.
Hungary's national team have only recently been punished by UEFA due to the discriminatory behaviour of their supporters - which also included the display of homophobic banners.
During Euro 2020 Hungary fans staged a march prior to their fixture against France urging players to stop taking the knee, while a number of French players were reportedly targeted with racist abuse.
UEFA ordered Hungary to play their next three fixtures behind closed doors, but their meeting with England comes under FIFA rule due to it being a World Cup clash, with a bumper crowd in attendance.
Asked ahead of the fixture whether he had prepared his players for a potentially hostile reception, England boss Southgate said: "We always prepare the team for everything really and we’ve done that this week.
“But we know we've had our own issues at home so we are not really focused on other countries, we are focused on ourselves and making sure we get our own things correct.”
It was only two years ago that England's match with Bulgaria in Sofia had to be stopped twice due to racist behaviour from home fans.
But Southgate would not be drawn on if his players would walk off the field should they be on the receiving end of more discriminatory abuse.
“I don’t think we should speak hypothetically," he added. "We know the experience we had before, but we’re going to Hungary preparing for a game against a crowd that will get behind their team and we’re looking forward to the challenge of the match. Everything else is speculation really.”
England topped their group heading into the match with a perfect record of three wins from a possible three, with Hungary just two points behind.
Southgate also admitted he was concerned England could face a stadium ban of their own following the behaviour of fans at Wembley for the Euro 2020 final.
“We still don’t know what the outcome of the investigation into our final is going to be and maybe we end up with a stadium ban," he said.
"I understand the question and focus outside but I always feel as if we shouldn’t look elsewhere until our own house is in order.
“Whilst we are always vigilant in preparing our team for whatever they may face, all of the issues you talk about very important ones, I have always been brought up that when I’m a guest somewhere I’m respectful of that, show that due respect, and that’s as I’d want to be treated if people were travelling to our country.
“The players understand the seriousness of the matters you talking about but I think we have a long way to go ourselves before we start comment or preempt what might happen in a game somewhere else.”
