Full-back Halfpenny damaged a pectoral muscle during his debut for the Super Rugby champions in a 21-19 defeat to Ireland's Munster on the New Zealand side's pre-season tour.
Halfpenny needs surgery and will be sidelined for the next three to four months, the Crusaders said.
"It is a real bummer for him," Crusaders' assistant coach Tamati Ellison told reporters via a video call from England.
"He will still help, even during his rehab period around some of the kicking and the game-driving for a few of our younger boys. He has been great there already."
The Crusaders kick off the defence of their Super Rugby Pacific title at the Waikato Chiefs on February 23rd. The final is in June.
The Christchurch-based side hope Halfpenny will be involved in the later rounds of the season. "We're expecting him to play, if the rehab goes well," Ellison said.
Halfpenny, 35, joined the Crusaders late last year after retiring from international rugby.
He made 101 appearances for Wales and won four caps for the British and Irish Lions.
