Crabtree was placed on the physically unable to perform list in July and has yet to be activated. The Bee reported that Crabtree fractured his foot during player-only workouts in June and underwent surgery before the start of training camp, according to a source.
Harbaugh said Crabtree has been "outstanding" in meetings, exhibiting a firm grasp of the team's offense, according to Comcast SportsNet Bay Area.
If Crabtree can't pass a physical before the beginning of the regular season in September, he must remain on the PUP list for six weeks.
Crabtree missed the entire preseason as a rookie because of a lengthy contract dispute. He again missed the preseason in 2010 after suffering a neck injury during training camp.
Missing training camp in 2009 slowed his rookie transition, and last season, the timing between Crabtree and quarterback Alex Smith was off early. Crabtree rallied strong to finish with 741 receiving yards and six touchdowns, but the 49ers went 6-10 and missed the playoffs for the eighth consecutive year.
In addition to the foot issue this year, Crabtree also openly challenged Smith's status as the starter when he arrived and downplayed the quarterback's efforts to organize offseason workouts.
Crabtree, the 10th overall pick in the 2009 NFL Draft, held out of his rookie training camp while waiting to approve his contract. After a 71-day stalemate, Crabtree agreed to a six-year deal with $17 million guaranteed.
"Offensively, as it relates to the backs and just overall with our offense, there are good snaps and there are snaps we want back -- mentally and physically," he said.
The Associated Press contributed to this report.