Shaqiri, 23, has been restricted to just three Bundesliga starts so far this season, while each of his four appearances in the UEFA Champions League have come as a substitute.
The Switzerland international's continued lack of game time has led to speculation over his future.
And Beckenbauer expects Shaqiri to find a new club when the transfer window reopens in the new year.
The 69-year-old told Sky: "Bayern have already sent out a signal and indicated to him that he can probably go in the winter break, when he wants.
"I think it's a shame because he is a great talent."
Shaqiri, who joined Bayern from Basel in 2012, has been heavily linked with a move to Serie A.
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