The 59-year-old insists that their proposed deal with the Russian energy giants will not adversely affect Schalke's existing agreement with the company
It was first reported last month that the Russian energy company was keen on linking up with Bayern in order to boost its profile in German markets.
Hoeness has now revealed that the two parties are talking but insisted that Bayern are not trying to undermine their Bundesliga rivals Schalke, who have been sponsored by Gazprom since 2007.
"If we cooperate with Gazprom, it would be in conjunction with Schalke instead of replacing them,” he told Sport Bild.
"I have also guaranteed this to my friend [Schalke chairman] Clemens Tonnies."
Schalke signed a new deal with Gazprom last May that will run until 2017.