Coach Jim Harbaugh said Monday that Morgan was scheduled for a "procedure." He was injured late in the fourth quarter of San Francisco's 48-3 victory against the Tampa Bay Buccaneers on Sunday.
"It's more serious than what I thought after the ballgame yesterday," Harbaugh said. "Josh is going to be out for an extended time, longer than we anticipated and longer than we hoped - longer than you can afford to have him out. ... I just feel sick for him and for our team. There's nobody you can afford to lose. Especially him, Josh was really playing well."
Morgan caught a 19-yard pass from backup quarterback Colin Kaepernick on fourth-and-3 and was tackled just short of the goal line - one of his five receptions for 75 yards Sunday for the NFC West leaders.
He grimaced in pain and stayed on the ground for several minutes as teammates gathered around in support. Fans at Candlestick Park chanted "Morgan! Morgan!" before he was carried off by Vernon Davis and trainers and then carted to the locker room.
San Francisco is already without receiver Braylon Edwards, recovering from surgery on his right knee. Harbaugh hopes to have him back Oct. 30 against Cleveland following the bye week.
"That's a good possibility," he said.
Harbaugh isn't counting out Morgan returning late this season or for a potential playoff game.
"That's a hope. We'll have a better idea after today, tomorrow and see where we're at to assess the situation," he said. "Josh was really coming into his own, catching his stride. I feel bad for him, feel bad for us. That's a tough loss for us."
The 26-year-old Morgan, a fourth-year pro out of Virginia Tech, has 15 catches for 220 yards and one touchdown for the 49ers (4-1). As tough as it was to see Morgan go down, Harbaugh didn't regret his decision to go for it on the play with a big lead.
For now, Harbaugh will move forward with Ted Ginn Jr., Michael Crabtree and Kyle Williams in the receiving corps along with someone brought up from the practice squad in the next day or so. San Francisco plays at Detroit on Sunday.
Tight end Delanie Walker likely will stay in his regular position but also could become an option. Walker had a touchdown catch in the rout of the Bucs.