Jordan Houghton is back with parent club Chelsea after suffering a knee injury in training for Doncaster Rovers.
The on loan midfielder damaged his knee in training with Rovers on Friday but travelled with the squad for Saturday's trip to Gillingham.
However, the injury worsened overnight and he returned to Chelsea for assessment over the weekend.
"Houghton took a knock on Friday in training," boss Darren Ferguson said.
"He travelled down with us, we thought he'd be okay. We looked at him on Friday night and he seemed okay.
"It was just a knock on his knee. Nothing to do with anything he's had before.
"We felt that if there was no more reaction to it by the morning then he'd be fine.
"But when we looked at it about half nine, there was a little bit more swelling on it so there was no way he was playing.
"He's gone back to Chelsea straight away.
"He'll spend the next few days with them and then rejoin us on Tuesday.
"I fully expect him to be fit for Milton Keynes next weekend."
Another absentee from Saturday's squad was Alex Kiwomya, who did travel with the team.
And Ferguson explained it was a selection issue that dictated Kiwomya's absence as he had a desire to keep the matchday squad as similar to the one that won at Blackpool, a game which the striker missed through illness.
"Alex has got to find a way of getting back in the squad," Ferguson said.
"I think it would have been unfair on everyone else if I'd have left them out."
Tom Anderson will be fit to face MK Dons on Saturday after recovering from a broken cheekbone.