It was responding to an advance summary of a report on Wednesday by the Handelszeitung paper which formed the basis of a number of news stories.
"This preliminary information, which contains wrong statements, was partially corrected by Handelszeitung for today's print edition," the bank said in a statement.
"However, the newspaper did not send the corrected version to the media, which has resulted in today's wrong reports in several newspapers," it said, adding it would use "all available means to defend its interests against the damaging statements that are without any foundation".
It did not specify which parts of the Handelszeitung story it was disputing.
The advance summary of the report said a dozen FIFA officials had accounts at Baer, but the print version speaks of a number in the low single figures.
Handelszeitung had no immediate comment on Baer's statement.
FIFA has been in turmoil since May when 14 soccer officials and sports marketing executives were indicted in the United States as part of a criminal investigation into the allocation of media, marketing and sponsorship rights for tournaments.
(Reporting by Michael Shields; Editing by Jason Neely and Keith Weir)
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