The 24-year-old went under the knife at the end of last year and had a screw inserted to try and repair a fracture in his foot.
The procedure appeared to have been successful but Kreuzer's foot problem flared up in the aftermath of Carlton's round one loss to Port Adelaide, causing him to be a late withdrawal against Richmond last Thursday night.
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The ruckman trained lightly this week but was still experiencing pain prompting more serious action to be taken.
"We have been monitoring Matthew’s foot this week and although he has managed to participate in training, he is still experiencing significant pain," Carlton’s football operations manager Andrew McKay said.
"His surgeon and our club doctor have determined it is in both Kreuzer’s and the club’s interests for him to have another procedure, to ensure he is fully fit to play a role in the later part of the season.
"Kreuzer is an integral part of our team and will be missed on the field, but we’re confident this is the best course of action going forward."
Surgeons will remove the screw inserted into the ruckman's foot, and replace it with a plate in the hope that it solves Kreuzer's foot issues once and for all.
"He'll have a bone graft on the inside of the fracture side, put a plate over the top and then have more bone graft filling in the deficit of the fracture that hasn't healed," McKay said.
Kreuzer admitted he was disappointed to miss the next 12-14 weeks.
“After chatting to the club doctor I know that this is the best way to get my foot right, so hopefully I can come back fitter and stronger and play a big role for the team at the business end of the season,” Kreuzer said.