The 24-year-old, who rejoined Cobblers on a season-long loan, was in agony after landing awkwardly on his knee in the closing stages of the 4-1 defeat.
He was visibly upset as he hobbled from the pitch, and on Monday Jon Brady confirmed the worst.
“Unfortunately we have had the diagnosis back and Callum will be out for the rest of the season,” he said. “He’s distraught and you really feel for him because he’s come back from a previous long-term injury.
“He was over the moon when he scored his first goal at Sixfields and he really added energy to us. We feel for him and we’ll support him 100 per cent because it’s very tough to take, not just for him but for everyone at the club.
“That’s now three long-term injures (Luke Mbete and Patrick Brough in addition to Morton) we’ve picked up in the last four games.”
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