The Northampton player-coach suffered a dislocated collar bone in a training ground collision.
"It's a blow for Andy," boss Gary Johnson told the club website.
"It was an innocuous challenge with one of our goalkeepers, he just fell awkwardly and we suspect he will be out for around six weeks."
Johnson may now offer a longer deal to Ashley Westwood, the 34-year-old central defender who has linked up with the Cobblers in recent weeks on an unpaid basis.