The Germany international was sidelined in August with an ankle injury which required surgery.
He was initially ruled out for four weeks, but could now be out for considerably longer with Muller-Wohlfahrt unable to give a precise date for his comeback.
"I saw Mario in my clinic earlier and things are improving, but I cannot say yet when he will be able to start training again," said the doctor to the Bild newspaper.
"We initially hoped it would take just four weeks, but unfortunately it is taking a bit longer.
"There are no complications, but such a recovery can take longer. You can never predict that in advance."
Gomez had pencilled in Tuesday night's clash with BATE Borisov in the Champions League as a potential date for his return to action, but he is not going to be seen in a Bayern shirt for at least a few more weeks.
"We are doing what is possible, but we must be patient," added Dr Muller-Wohlfahrt. "But I am not worried. He will be back, it just could take time."
When Gomez does return, he faces stiff competition for his place in the starting XI.
Mario Mandzukic has scored six goals in six Bundesliga games since taking Gomez's place.