The Bayern Munich sporting director was asked about Ballack's intervention following Saturday's 2-2 draw with Borussia Dortmund. Ballack, who represents Karl, had criticised the club's public comments about the 18-year-old and accused its leadership of making the teenager a target.
Eberl questioned the capacity in which Ballack had made his remarks, pointing to his roles as both a television pundit and Karl's representative.
“Honestly, I find it difficult when this kind of discussion is conducted through the media. Did he say that as a DAZN pundit or as the player's agent? I don't know exactly,” Eberl told Sky.
The Bayern executive nevertheless stressed that the club remain impressed by Karl's development, despite recent criticism of his performances and conduct away from the pitch.
“We saw him as a great talent last season, someone who made fantastic progress. He was not in London at the Ballon d'Or among the nominees for the best young players for no reason, and that made us very happy,” Eberl said.
The youngster had also experienced a difficult period after missing the World Cup, according to Eberl, who acknowledged that his return presented challenges.
“He has missed the World Cup as a young person. Then he comes back. It was complicated for him,” the sporting director added.
Eberl also defended the club's earlier assessment of Karl's performances, arguing that Bayern's comments were intended to recognise a dip in form rather than undermine the teenager.
“Those of us working in sport knew that a development like this can have a dip. It doesn't always go straight upwards. That is all we said,” he explained.
“We said that his performances against Freiburg and Magdeburg showed he was on the right path. And we are impressed by how this young man is now putting that behind him.”
The dispute began after Bayern figures, including honorary president Uli Hoeneß and Eberl, publicly expressed concerns about aspects of Karl's conduct and public image. Ballack subsequently defended his client, arguing that the club's comments risked turning him into a target.
The disagreement has brought an unusual public debate around one of Bayern's most promising young players. Eberl's latest comments suggest the club are keen to distinguish criticism of a difficult period from any doubts about Karl's long-term potential.