Steven Motlop and Daniel Menzel could miss three or four AFL matches as Geelong aim to ensure they are ready for the finals.
Motlop and Menzel went out of the Cats' side last week and there is no way they will return for the big home game this Friday night against resurgent Sydney.
Motlop was listed as being managed and Menzel was general soreness.
"They have made strides forward and probably in previous weeks, if they were in the same physical state, they might have played," Scott said.
"But we're in a phase where we want to give them the best chance to be healthy later in the season.
"As important a game as this one is, we've resisted the temptation to bring those guys back.
"It could well stretch into three or four weeks."
The Cats are adamant that Motlop's absence is due to a physical problem, rather than just form.
Patrick Dangerfield's suspension also meant the second-placed Cats will be without him for the first time since the Brownlow Medallist joined them last year.
"It's going to make it more challenging for us, but not impossible," Scott said of the star midfielder's absence.
Scott noted that Geelong would have eight or nine new players compared to their team late last season.
"It is a new team and that's daunting on one level, but it's exciting on another," he said.
With Lincoln McCarthy possibly sidelined for the rest of the season, Scott said the Cats could upgrade Jamaine Jones or Jack Henry from their rookie list.
Sydney are sixth and are the league's most in-form team.
They have only lost twice since round six - both times to Hawthorn by six points.
Scott said while they obviously look at how Hawthorn beat Sydney, Geelong must remember what makes them a good team.
"Sometimes you can have a look at one team beating Sydney and think 'all you have to do is play the way that Hawthorn did," he said'.
"I for one think when I look at it, Hawthorn play their way against Sydney and it works."
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