The new rule, announced on Tuesday, will also see runners' time on field restricted.
It is aimed at reducing on-field clutter, and preventing runners from coaching while on the ground.
Scott became the first senior coach to publicly question the change.
"It's an interesting move to me," the Kangaroos coach told NMFC.com.au.
"I didn't think we needed to go down that path.
"Clearly the powers-that-be are keen to reduce the amount of officials on the ground, [but] there'll be the same number of
officials, because there was only ever allowed to be one runner on the ground anyway."
Scott compared the theory behind the change to the introduction of a cap on player interchange rotations – a rule that will also be introduced for the 2014 season.
"We are trying to fatigue our runner so he can't get out there as often, but in a game where you don't have time-outs and you only have limited opportunities to talk to your players, the runner is pretty vital," he said.
"I'm sure we'll cope, but it's going to limit the type of runners we can use because they are going to have to be pretty fit.
"It makes more sense to me to have fresh runners, so they can sprint on, give their message and sprint off.
"Now you are going to have a runner who's literally tired and can't get on and get off as quick as he used to.
"I hope we don't defeat the purpose of the rule change."
Scott credited the AFL with moving to prevent on-field coaching by runners – something he agreed needed to be stamped out – but feared the new rule would penalise clubs that were doing the right thing.
"As a rule of thumb, I don't like to deliver a message that takes the runner longer than five seconds to deliver anyway," he said.
"So as a club, we like to get the runners on and off very quickly."
