Hoeness shocked Germany last month when he said he had voluntarily alerted tax authorities in January to a Swiss bank account he held, throwing the former West Germany international's future into doubt.
He is now under investigation for suspected tax evasion and, if convicted, he could be sentenced to jail. The admission, which also has political ramifications, came just as Bayern regained the Bundesliga crown from Borussia Dortmund.
"In the interest of Bayern Munich... the board of directors has, after an intensive discussion, decided that Uli Hoeness should continue to carry out his role as the Bayern Munich club president," the club said in a statement on their website.
Bayern added that the club "should concentrate fully and entirely on achieving the sporting goals in the Champions League final on May 25 and the German Cup final on June 1."
"Uli Hoeness has expressed his regret to the club over the case and apologised," the club said.
"The board of directors will continue to observe the situation and deal with any new findings on the topic."
Hoeness, 61, had been an eminent figure in Germany, both for his managerial prowess in building Bayern Munich into one of the world's most successful football clubs and his straight-talking views on politics and business which made him a popular guest on talk shows and in the chancellery.
Hoeness, who became Bayern's general manager in 1979 at the age of 27 after a knee injury ended his playing career, has close ties to Chancellor Angela Merkel and her Christian Democratic party and the situation has hurt both in an election year.
He has also been a stern critic of FIFA president Sepp Blatter, saying last year that the Swiss should be "deposed" if he failed to clean up football's governing body.
"I made a foolish mistake, a giant blunder that I'm trying to correct as best as I possibly can," Hoeness told the online edition of Die Zeit weekly last week.
