Team spokesman Bob Lange said the 49ers immediately reported the "oversight" to the league office after it happened Monday afternoon. It's unclear if the team will be penalized.
NFL spokesman Greg Aiello said the league was investigating the situation.
Crabtree, the 10th overall pick in 2009 NFL Draft out of Texas Tech, has missed his third consecutive preseason, this time while nursing a left foot injury.
First-year 49ers coach Jim Harbaugh said Sunday he hopes to have the receiver back in an official capacity this week, although Crabtree wasn't in uniform when he caught throws from quarterback Alex Smith at the start of Monday's practice before general manager Trent Baalke intervened and had him stop participating and then leave the area.
"We are looking into it. We appreciate Trent Baalke contacting our office to report what happened," Aiello said in an e-mail. "Our understanding is that it occurred during warm-ups and that Michael Crabtree did not participate in practice."
Crabtree hurt his foot during workouts led by Smith in June during the NFL lockout. He missed the 2010 preseason with a neck injury one year after a 71-day contract stalemate as a rookie.
Crabtree, 23, hasn't talked to reporters so far this preseason.
Crabtree, who has long had the reputation of being a diva, posted 55 catches for 741 yards and six touchdowns last season, when San Francisco went 6-10. He was angrily confronted by tight end Vernon Davis during an early September practice last year, and then-coach Mike Singletary had to step between them.
Copyright 2011 by The Associated Press