Lee fell awkwardly late in the game on Tuesday night after coming to collect a cross and was replaced for the closing stages by summer signing Richard O'Donnell, who now looks poised to make his full debut when the Spireites resume League Two action at York on Saturday.
Following the 2-1 win over the Latics, caretaker manager Tommy Wright said: "It's a concern. He went straight to hospital and it looks like it could be a bit of ligament damage.
"It's a massive blow because we all know that Tommy is a top-class keeper, but hopefully he won't be out for too long."
Wright added: "We have to deal with the situation and Richard O'Donnell is a good keeper and he'll get his chance now, and he'll have to take it."
Wright also confirmed that defender Nathan Smith is to have an operation on the ankle problem that has been troubling him recently.