Scharenberg has had ongoing foot issues which have reduced the 18-year-old's pre-season contribution and saw him spend considerable time completing a scaled back, 'off-feet' training program.
But the problems have persisted and he will undergo surgery to remove a small bone in a toe in each foot, a procedure which will put his recovery back until at least mid-year.
"It doesn't drastically change the scenario for Matthew, who only turned 18 a few weeks before the draft," Collingwood Director of Football, Rodney Eade, said.
"He is a very talented player but he is young and we were always taking a long term approach with him. There was a small amount of lingering pain and with the operation he will have some certainty of an outcome.
"There is no real time frame on his return but all going well he should be running and seriously preparing to play in late May."
The Pies had learned earlier in the week that Adam Oxley will miss six weeks with an ankle problem.
The news is also bad for St Kilda's Sam Gilbert, who has suffered a stress fracture in his left foot and will miss up to six weeks.
Gilbert has had a screw inserted and faces a race against time to be ready for the Saints' Round 1 clash against Melbourne.