The Germany international underwent an operation on his right ankle in June, but the problem has flared up again and will keep Schweinsteiger out until the new year.
Media reports over the weekend poured doubts over Schweinsteiger's ability to return from his latest setback, having suffered four similar issues in the past year.
However, the club insist the 29-year-old will be back in peak fitness when he returns after the German mid-season break.
Chief medical officer Hans-Wilhelm Müller-Wohlfahrt told Bayern's official website: “Unfortunately there has been a large-scale media debate since last weekend regarding Bastian Schweinsteiger's state of health, conducted in a manner which is inappropriate and untenable with respect to the player.
"Opinions are being expressed by colleagues who have no access whatsoever to specialist information, including diagnoses and visual material.
"The injury concerns an extra-articular condition [situated away from the joint].
"The ankle joint itself is not affected. The post-operative prognosis may be regarded as very favourable.
"Bastian Schweinsteiger's fitness for the year 2014 is not endangered in any respect."
Schweinsteiger was a key figure in Bayern's treble-winning side last term and had made 17 appearances under Pep Guardiola before his latest lay-off was confirmed.