Latics boss Steve Bruce told the Wigan Observer: "Cywka is out until next season. He's torn his knee ligaments in the reserves and he'll need an operation.
"It's a real shame for the kid because he's been playing very, very well for the reserves."
Cywka was said to be on the verge of breaking into the first team, and had made one appearance as a subsitute in the FA Cup third round defeat to Tottenham back in January.
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