Some England supporters in Dortmund on Wednesday could clearly be heard singing songs about World War I and II, with the chants loud enough to be picked up by television microphones.
Hours after the attack in London, and with the British national anthem politely observed by the home crowd, jeers could be heard when the German anthem was played.
Germany won 1-0 thanks to Lukas Podolski's stunning second-half goal in his final international appearance.
"Over the last 20 years English football fans have built a worldwide reputation for our passionate support and the vocal backing we give to our teams," said the Football Supporters' Federation.
"England's travelling support is made of people of all ages from a range of clubs, many of whom have worked hard in recent years to improve our standing abroad and have expressed concern to us about these chants.
"We don't want to regress to a situation where that reputation is tarnished by the actions of a minority."
England manager Gareth Southgate, asked about the chants after the match, said he had not heard them "but it has been mentioned to me".
"Obviously our travelling support in terms of number and the way they back the team is brilliant," he said.
"We would encourage them to do that in the right way at all times."