The slippers were loaned to the museum in 2005 by movie memorabilia collector Michael Shaw.
The shoes stolen from the museum were insured for $1m.
The museum suggested to Shaw that they store the slippers in a vault each night.
A pair of ruby red slippers, produced for Judy Garland to wear in the Wizard of Oz, have been discovered by police over a decade after they were stolen from the Judy Garland Museum in Grand Rapids, Minneapolis.