The NFL changed the rules in the off-season after many teams complained about the lack of clarity concerning the role of the quarterback in the system.
Harbaugh told reporters: "I know what the rules are, I know how they've been explained, but there's still some gray area. When you start using words like 'clearly' — he clearly doesn't have the ball — what does that really mean?
"To me, he's a quarterback until he leaves the pocket as a running threat. I think it's flawed, the way they've got it now."
San Francisco open their regular season campaign against the Green Bay Packers on Sunday.