Michael Becker, a close adviser to Ballack since 1999, made the remarks two months before the World Cup, according to news magazine Der Spiegel.
Writer Alexander Osang recounted an interview he had with Becker prior to the South African tournament in which the agent allegedly told him which of the players in the team were gay, making a reference to one who was "half gay."
Becker later told a group of players and managers there was a former national player who was going to expose a "bunch of gays" within the national team.
Osang said homosexuality was "a synonym for anything that Becker did not understand."
Becker has since said that he was "misunderstood" and that the interview was not "authorized" - a right often accorded interview subjects by German newspapers to check their quotes before publication. But neither did he confirm or deny that he made the remarks.
Osang said Becker had told him "unbelievable stories that I took down in my notebook and Becker didn't seem to have anything against me doing so".
Germany were a revelation at the finals in South Africa, playing with flair and energy in the absence of Ballack, who was injured while playing for Chelsea in the FA Cup final in May.
The whole issue of gay players in the Bundesliga is a sensitive issue in Germany. In March former football manager Rudi Assauer provoked outrage by saying there is ‘no place' for gay players in football.
Assauer, who was boss of Schalke in Germany, said: "Perhaps they are OK in other sports but not in football.
"If a player came to me and said he was gay I would say to him: 'You have shown courage.' But then I would tell him to find something else to do.
"That's because those who out themselves always end up busted by it, ridiculed by their fellow players and by people in the stands. We should spare them these witch-hunts."
His outburst is set to enrage world footballing authorities who are making concerted efforts to rid the game of homophobia.
Asked whether he had ever met a gay footballer during his many years as both player and manager, 65-year-old Assauer replied: "No, never.
The German FA (DFB) later said his comments were reprehensible.
There has never been an openly gay top-level footballer in Germany. Erfurt Marcus Urban did come out after his playing career was over, though he was a regional division player and never represented the national team.