Linked with West Ham and Napoli, Toni has had limited opportunities under new Bayern boss Louis van Gaal and his frustration surfaced during the recent game against Schalke when he left the stadium after being substituted at half-time.
Beckenbauer is a fan of the Italy striker but concedes he will be leaving the Allianz Arena in the near future.
He told Gazzetta dello Sport: "I like Toni as a player and as a person. He has done a lot in Munich and Bayern have given a lot to him.
"I would like to keep him but if he wants to go then he should go."