Wilson said on Channel Nine's Footy Classified on Monday night that North medical services director Steve Saunders had been overruling the club's doctor since joining the Kangaroos ahead of the 2011 season.
Scott said on Wednesday that North would be seeking an explanation of Wilson's comments, which he described as potentially libellous.
"One thing that we are concerned about is that there are false accusations that any one of our staff would overrule a doctor. That is simply a lie," Scott said at Aegis Park.
"It's very dangerous territory when you start making those accusations without any evidence to back it up. I can categorically say that's not true.
"And, unfortunately, when Caroline Wilson speaks these days about North Melbourne most people think that it's just pursuing a personal vendetta that she's had against James Brayshaw for a long time.
"Unfortunately for us when Caroline speaks about our club I think most people probably tune out."
Asked whether the club would consider legal action against Wilson, Scott suggested the club would first ask Wilson to explain her comments.
"I think professional credibility and reputation is everything and when that's brought into question I think you've got a right to defend yourself," he said.
"So I think we'll be seeking explanation of those comments."
Brayshaw said on Saturday the AFL had to come up with a better model than simply insisting the club doctor have the final say on medical matters, given club doctors were only part-time employees and other sports science and fitness staff were now full-time.
But Scott was adamant North fully supported the club doctor having the final say on medical matters.
"There can be no other way. That's certainly (been the case) in my time at North Melbourne," Scott said.
"The doctor has had absolute final say on all medical decisions and that is cut and dried and that's always been the case.
"So to suggest otherwise is libellous."
Scott said North was not concerned about its 2011 supplements program in the wake of last week's revelations that their club doctor at the time, Dan Bates, had subsequently in his role as Melbourne club doctor consulted with controversial sports scientist Stephen Dank on player supplements.
"There's an obvious link … (but) I can't believe it's a news story," Scott said.
"We didn't hide the fact that Dan Bates was our doctor for a year. Once the news broke about the link between Dr Dan Bates and Stephen Dank we made contact with Dan and sought a written assurance that he'd had no contact with Stephen Dank in his time here as an employee.
"He has since provided that in writing that he's had no contact there. We welcome any potential investigation as to Dan's role while he was our doctor."
Scott said North had been in contact with the AFL since the Bates revelations, saying the AFL had assured the club it was "really confident" in North's medical processes and protocols.
"We were always in full contact on that with the AFL and I'd suggest instead of asking me ask Andrew Demetriou or ask Dr Harry Unglick, the medical officer at the AFL, if they have any concerns with our medical processes and procedures.
"Because we've been open and honest and we've disclosed absolutely everything to the AFL, so we have no concerns."
Nick Bowen covers North Melbourne news for AFL.com.au. Follow him on Twitter: @AFL_Nick
