Scott said Petrie had trained well during the week and was cleared to play by the club's medical staff.
"He got medical clearance from the surgeon to play," Scott said. "We have had training sessions with him where he looked really strong but clearly he wasn't right today.
"Obviously we wouldn't risk him if it was going to do any damage in the second half, but the medical guys were pretty confident he could go out and play full forward and when it became evident to me and probably everyone at the ground he just wasn't right we took him off.
"We will assess him and see how he is but I have no word at this stage as to just what is wrong, whether it's a new injury or an aggravation of the old one."
Scott was bitterly disappointed by his side's effort against the Sydney Swans at the SCG on Sunday as they fell from a tie for eighth spot on the AFL ladder and further away from September action.
Scott labelled his team "mentally injured" by the result after they trudged off the SCG with their heads hanging low.
"We knew what an important game this was for us and we didn't come out and compete as we had hoped," Scott said.
Scott, who held an extraordinarily long team meeting post match couldn't hide the way he felt after a below par effort where the Swans' midfield and backline strangled North Melbourne and thwarted their attack, which resulted in only seven goals.
"It was a really important game for the football club, we came up, felt really well prepared and we really let ourselves down," Scott said.
"It's a really disappointing day for the footy club, but we've got a really good opportunity to get back to Melbourne and rectify it next week.
"I thought the Sydney Swans ran really hard today they ran a lot harder than us and really taught us a lesson in that regard.
"The fact that we couldn't get our hands on the ball often enough when it mattered and that we still got the ball inside 50, 50 times, which should be enough to kick enough goals, but they were really poor quality entries," Scott said.
With North Melbourne facing a red-hot Richmond next week, they would want to perform or they risk their season unravelling.
