Harbaugh did not specify what the injuries are but said Crabtree's is not related to his foot or achilles, which he tore last May.
ESPN's Josina Anderson quoted a source who spoke about Crabtree's undisclosed injury.
Source familiar with #49ers WR Michael Crabtree on his undisclosed injury that will sideline him for now: "I think he has a sore hamstring. Nothing too serious right now." The source added, "I think they want to hold him back a bit to be cautious."
Crabtree, 26, was limited to only five games last season due to the achilles tear. He caught 19 passes for 284 yards and one touchdown. In 2012, Crabtree recorded 85 receptions for 1,105 yards over 16 games.
Lloyd, 33, signed a one-year contract with San Francisco in April after taking a year off from football. He caught 74 passes for 911 yards in 16 games with New England last season.
Lloyd is expected to compete for the team's No. 4 receiver spot.
The 49ers went 12-4 and finished in second place in the NFC West last season before falling to Seattle in the conference championship game.
- Chris Johnson