The retailer said the name was being phased out on the packaging of products that did not meet the Protected Geographical Indication criteria.
The products are believed to be those made by own-label supplier Northern Foods, which manufactures the pies outside the area.
The supplier is currently in a long-running PGI legal battle with the Melton Mowbray Pork Pie Association. Its appeal against the association's application for PGI status has reached the European Court of Justice and could take two years to resolve.
A spokeswoman for M&S refused to comment on whether the move was a vote of no confidence for Northern Foods' appeal.
She said its remaining Melton Mowbray pork pies were in line with current legislation and were produced traditionally in the Melton Mowbray area.
Northern Foods said it was a matter for the retailer and would not comment. Earlier this month Northern Foods said it was planning to sell its chilled pastry division, which makes the pork pies, as part of a radical overhaul of its business.