Cotterill was expected to be among the substitutes at Sheffield Wednesday on Boxing Day after recovering from a knee injury sustained against Blackburn Rovers, but the midfielder suffered hamstring tightness and was left out.
"His knee’s fine and he was due to be on the bench for Sheffield Wednesday," said Rowett.
"He just felt his hamstring tighten up towards the end of training on Christmas Eve.
"We left it up until Boxing Day and we didn’t feel it was worth the risk at that point and then of course with the MK Dons game coming so soon after, we just felt the benefit for him to get a full weeks training in.
"It might be too soon for the Brentford game, but we hope he’ll be alright for the Bournemouth cup game.
"Obviously he hasn’t been tested fully yet, but his knee’s been fine. Often you get a little bit of muscular injury after a while, it’s not uncommon."
Cotterill's setback was a blow for Rowett, who believes the Wales international is a vital part of the squad on and off the pitch.
"We’ve got a lot of good players, but you saw the impact Clayton had back into the team," added Rowett.
"I think you can look at someone like Cotts in the same light and Paul Robinson of course that came in and did so well.
"In games like that (MK Dons) where you dominate and only win 1-0, the likes of David Cotterill who’s a goal threat, he creates goals as well, so I don’t think you can have too many of those players in your squad.
"Certainly he’s been a big miss.
"I think with someone like Cotts, he’s bubbly and bright around the place, he’s good fun.
"And sometimes training is a little bit quieter without him!
"He has an important role to play for us and it’d be good to get him back out on the pitch."