Beckenbauer: Shaqiri can 'probably' leave Bayern
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.