TMZ has video of the alleged incident, which shows a burly shirtless man beating someone who appears to be LaBeouf, 25, who is lying on the sidewalk.
The actor is seen getting up and trying to chase the unidentified man, but is held back by a friend, who tells him, "You gotta lay low right now."
According to Vancouver radio station News1130, LaBeouf was having a drink at Cinema Public House downtown when the alleged incident occurred.
"It is not clear what provoked the attack, but Shia threw the other man to the ground inside the bar," according to the local report. "Security personal then took both parties outside, where the ... man ripped off his shirt and started punching Shia."
The actor's rep did not immediately respond to calls for comment.
The Transformers star is in Vancouver to film The Company You Keep.
He was photographed biking on Sunday around the city, showing no discernible injuries.