In an added blow, Duffie, who missed last year's premiership win with a major shoulder injury, also needs another shoulder reconstruction.
Kiwi Duffie was returning from a shoulder dislocation in the NSW Cup on Saturday.
But just minutes into his comeback game, he tore the anterior cruciate ligament in his left knee.
Subsequent scans of both the knee and shoulder have revealed he needs reconstructions of both joints.
"Everyone is totally shattered for Matt - he has had absolutely no luck," Storm football manager Frank Ponissi said.
"Nobody has worked harder than Duff over the past few years, especially returning from a shoulder reconstruction and another shoulder operation in the last 18 months.
"Understandably, he is totally gutted by the latest setback."
The Storm hope the 22-year-old will be ready for the start of the 2014 season.
The knee operation will be today and the shoulder surgery in several weeks.
- AAP