Michael Becker has landed in trouble after allegedly giving an interview to der Spiegel in which he made the remarks.
Journalist Aleksander Osang subsequently wrote: "All sports journalists seemed to already know the alleged homosexual conspiracies enveloping [coach Joachim] Loew's team. The rumours accompanied our team to South Africa and evidently belong to the team."
Becker insists that the interview was not authorised, and has neither confirmed nor denied the comments.
Loew said he would not "stoop so low" as to comment on the allegations.
Meanwhile Ballack has given a hands-off warning to stand-in skipper Philipp Lahm.
Ballack was ruled out of the World Cup after suffering an injury in May's FA Cup final.
And Lahm stepped up to guide Germany to the semi finals of SA2010.
After the World Cup he said that he was keen to keep the armband.
But Ballack insists he wants to stay in charge.
"This is no issue for me," he said. "I am the captain."
Lahm has more pressing matters on his mind after getting married to girlfriend Claudia Schattenberg on Wednesday near Munich.