Herbert Hainer formally succeeded Uli Hoeness as president at Saturday's (AEDT) AGM, assuming the role amid the search for a full-time replacement for Niko Kovac.
Hansi Flick will continue in a caretaker capacity for at least the rest of 2019 while the Bundesliga champion weighs up its options.
Guardiola, along with Erik ten Hag and Thomas Tuchel, is one of three men being considered, according to Sport Bild, and Hainer has great respect for the Spaniard, whose contract with Manchester City runs until 2021.
"The board of directors will try to get the best coach for Bayern Munich," Hainer said.
"When I say the best, it means, on one hand, a coach who we want to have and, on the other, one who is available.
"Pep Guardiola is a great coach but he has a contract with Manchester City.
"For now I would say, let's wait until the board comes to us. Then we will deal with the options. But in principle, we want to have the best coach at Bayern Munich."
Guardiola spent three seasons in charge of Bayern before leaving for Premier League side City in 2016.
The Bavarian outfit won three Bundesliga titles and lifted the DFB-Pokal twice during his time at the helm.