Teams this season have struggled to win following the bye, with nine teams losing and only two, Geelong and Hawthorn, winning in the next round.
West Coast and St Kilda also won after their respective byes, but they were playing teams also coming off a week's break.
Malthouse said on Thursday Collingwood had been preparing for the bye for more than six months.
"We certainly won't be saying, win or lose, 'It's the bye's fault'. That's without exception; we will not be saying that," he said.
"You can be a little bit scratchy early perhaps but that's what you train for. You train to get that scratchiness out.
"When the draw came out in late October we factored it in accordingly, so it's been no surprise to us with how we've trained and no surprise about how we've come up."
Malthouse said the management of the players over the weekend off was decided on a case-by-case basis.
"Some players needed a breather, some needed to be topped up, some needed to be told not to come in. It's an individual training program over that period," he said.
"A lot of players went back home, for instance, when they're non-Victorian players, which is fantastic for them to see their family."
The Magpies face the Cats at the MCG in the battle of the competition's two undefeated sides.
Malthouse said the 'Chris Scott' brand of football had been impressive, and the Cats' strength was that they had remained largely unchanged over the past few years.
"Six from six - it's a fairly effective brand," he said.
The loss of Gary Ablett had been covered, not necessarily by one player, but by several.
"So their structures are very similar but they do defend differently, and their offensive line is different to what last year's was at stoppages.
"It's a matter of every club looking at it, weighing it up and seeing whether or not our assessment of them is exactly the reality of how they structure their players."
Malthouse said it was unlikely his team would be able to become the first to go through a home-and-away season undefeated.
"I'm on safe betting saying no," he said.
"It can only be a great side that can do that, and we've seen some great sides. It's a very tall ask."
Ben Johnson has been ruled out with the back spasms that troubled him against the Western Bulldogs while Nick Maxwell will face a further fitness test on Thursday afternoon.
If he passes, he'll be named in the side and assessed again on Friday morning.
Malthouse also said the Pies would not rush ruckman Darren Jolly back ahead of schedule after knee surgery.
