Mandzukic has been subject to rumours linking him to Arsenal, and with Robert Lewandowski set to join Bayern in the summer, the Croat's position could be under threat.
The 27-year-old has scored an impressive 12 goals in 20 appearances for the Bavarians, who are currently seven points clear in the Bundesliga with one game in hand over nearest rivals Bayer Leverkusen.
Beckenbauer told German sports magazine 11freunde: "Mandzukic could pack his bags. I see Lewandowski in the attack, his playing style is suited for (Pep) Guardiola's ideas than that of Manduzkic.
"There are even more reasons why he could leave - even without him, Guardiola could still count on Thomas Mueller and Mario Goetze in attack."