The 25-year-old sustained the injury to his left knee in training and will go under the knife next week.
The news will come as a massive blow for Ange Postecoglou and the Socceroos with Kruse becoming a key figure in the national side over the past year.
The winger has been capped 27 times for his country and with Australia set to face Chile, Spain and the Netherlands in Brazil the timing of the injury couldn't be worse.
A Leverkusen statement read: "Robbie Kruse suffered a tear of the anterior cruciate ligament in his left knee in training and thus is likely to be missing for Bayer 04 in the entire second half of this season."The Australian International picked up the injury on Friday at training, today (Saturday) an MRI scan showed the worst results."
Kruse moved to the BayArena from Fortuna Dusseldorf in the close-season and has made 21 appearances for Leverkusen this season, scoring three goals.