The Cobblers centre-back has missed the club's last two matches due to the tendon complaint sustained in the 2-0 home defeat to Plymouth earlier this month.
And boss Chris Wilder has revealed he will be without his influential leader for the remainder of Town's uphill battle for Football League survival.
"It is a major blow and he will undoubtedly be a big miss for us," Wilder told the club's official website.
"I've been really impressed with Lee, not just as a player but as a personality and it is times like this when you want your big characters who relish the challenge.
"Lee is definitely a big character but it's something we've just got to deal with and he's now just got to focus on getting ready for pre-season.
"I don't want to make too many more changes to the squad because we've done that now but with Lee's injury that might be an area that we do look at.
"It's a key area and it's important that we can be as strong as possible in that department."
- Sports & Recreation
- Chris Wilder