Arsene Wenger was linked with the vacant head coach role following the departure of Niko Kovac a couple weeks ago.
Guardiola was surprisingly linked with a return this past week, but Hainer says the Spaniard has a contract with the Citizens.
"The board of directors will try to get the best coach for Bayern Munich," Hainer said, as per Sport1 .
"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."