The Indianapolis Star had reported Wednesday that Mathis would miss some games, and Manusky confirmed the report when he was asked about it Thursday.
"It would have been great to have him up this week. But the next guy's got to stand up and go out there and perform at a high level," he said.
Mathis twisted his left knee in the fourth quarter of the Colts' comeback victory Sunday over the Packers.
He leads the Colts with five sacks and has recorded a sack in seven consecutive games dating to last season.
The Colts also will be without starting running back Donald Brown against the Jets Sunday after he had surgery to repair torn cartilage in his knee. Rookie Vick Ballard is slated to make his first start.
Information from AFC South blogger Paul Kuharsky and The Associated Press was used in this report.