The Millers agreed an extension to the player's month-long stay at New York, but Frecklington, 27, suffered a back injury during Tuesday night's 3-2 defeat to Wycombe.
The extent of his injury will be assessed, but it could result in him returning to London Road.
"We'd agreed that Lee Frecklington was extending and we are going to have to look at that now," said boss Steve Evans.
"He was staying but has had back spasms after taking a knock on Saturday.
"He trained okay on Monday but took a whack during an innocuous challenge and he had to come off. So we will wait and see."