"Through my tax consultant I filed a complaint about me in January 2013 with the tax authorities," Hoeness told German news magazine Focus. "It was in relation to a Swiss bank account of mine."
Munich's prosecutor's office confirmed there was an ongoing procedure in relation to the complaint filed by Hoeness but gave no details of the amount involved.
By filing a complaint about possible tax evasion, culprits in Germany can sometimes expect more leniency and reduced fines.
Bayern sports director Matthias Sammer said the affair would not affect the club as it prepares for a Champions League semi-final against Barcelona on Tuesday.
"That is a personal issue. We will not comment on this and it also does not weigh on us," Sammer told reporters.
Bayern have already clinched the German league title this season and are also in the German Cup final.
Hoeness is a high-profile figure at Bayern, having served as a player during the 1970s, a period of great success.
He then spent 30 years as the team's general manager before being elected president of the Bundesliga's richest and most successful club.