Bayern chairman Karl-Heinz Rummenigge said that suggestions Schweinsteiger was a "little boss" were impertinent and outrageous, although he also told "Schweini" he was wrong for losing his cool in Thursday's media conference.
"It's outrageous and impertinent that a man with such an impressive sporting curriculum is sneeringly refereed to as a "little boss" and discredited in this way," Rummenigge told Bayern's website.
"We understand that Bastian Schweinsteiger wants to defend himself although his choice of words, in this emotional situation, were out of order and he knows that."
The episode started on Wednesday when winger Arjen Robben suggested Bayern had lacked a real leader since his fellow Dutchman Mark van Bommel left to join AC Milan in January.
"We have our captains but Mark van Bommel was a real leader and that sort of player is missing now," Robben said in an interview.
Team captain Philipp Lahm admitted he was annoyed by Robben's comments. "I think I'm a good captain and I will speak to Arjen to find out what he meant by that," he said.
The episode comes with Bayern struggling to qualify for next year's Champions League.
They are currently fourth in the Bundesliga and need to finish third just to make the qualifying round.
Hanover are third, one point ahead of Bayern who host Schalke on Saturday.
Failing to reach the Champions League would be a devastating blow for Bayern with next season's final at their own Allianz Arena.
