Leverkusen bounced back from Wednesday's 5-0 home defeat by Manchester United with a 3-0 win over Nuremberg on Saturday but their relief was offset by concerns about the former West Germany striker.
"It's painful news. Rudi Voeller was not able to attend the game due to renal colic," the club said on their website, adding he had been taken to hospital.
Renal colic is caused by kidney stones and is very painful.
Leverkusen, third in the Bundesliga last season, have surpassed expectations with their domestic campaign this term and are second in the table, four points behind leaders Bayern Munich.
But Wednesday's Champions League debacle, on an evening when Leverkusen made a rare free-to-air television appearance usually reserved for Bayern or Borussia Dortmund, led to more soul-searching at a club often nicknamed "Neverkusen".
Voeller launched an angry tirade at the club's critics during a news conference on Friday and was also dismissive of internal worries about their image.
"The whole internal discussion about our image is absolute nonsense," he said. "We make ourselves out to be smaller than we are."
Saturday's win helped resume normal service at Leverkusen, who have often been labelled a "plastic club" by supporters of other teams who say Bayer have no real fan base.
Coach Sami Hyypia was relieved to put the United debacle behind his team, who have won 11 out of 14 league games this season and could still make the Champions League knockout stage.
"It was important to win today," he told reporters. "The preparation after the match against Manchester United was not so simple. But after that disappointment we showed character."
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