Hoeness, who played for Bayern and West Germany in the 1970s, has admitted to evading taxes and said he received a personal loan from former Adidas boss Robert Louis-Dreyfus, who died in 2009 after a long battle with leukaemia.
"We will remain a shareholder of FC Bayern Munich," Adidas Chief Executive Herbert Hainer (pictured left, with Hoeness) told journalists on Friday after the group reported first-quarter results.
The loan from Louis-Dreyfus prompted speculation in the German press that the friendship between the two may have helped Adidas win an extension of its sponsorship deal with the club in 2001, as well as influenced Adidas' purchase of a 10 percent stake in Bayern Munich in 2002.
Hainer said on Friday the stakeholding talks began only in early 2001 and that Louis-Dreyfus had stepped back from the day-to-day running of the company in 1999 because of his illness.
Hainer also said that neither he nor anyone else at Adidas knew of the loan to Hoeness.
"We have researched this internally and from a compliance point of view we are completely clean," Hainer said.
Adidas now has a stake of nine percent in Bayern, which is one of Europe's wealthiest clubs and aiming to become European champions for a fifth time later this month in a final against German rival Borussia Dortmund.
Hoeness shocked Germany last month when he said he had voluntarily alerted tax authorities in January to a Swiss bank account he held. The admission came just as Bayern regained the Bundesliga crown from Dortmund.
The scandal has also hurt Hoeness' friend Chancellor Angela Merkel in an election year. He earlier this week told a German weekly that he hoped his decision to come clean would help repair the damage.
Hainer urged the press and public to hold fire on judging Hoeness until the results of the investigation into his tax affairs was complete.
If convicted, Hoeness could be sentenced to jail.
"We must wait to see what comes out and then we will sit down with Hoeness and FC Bayern afterwards, but we will not speculate on that now," he said.
