Under the new guidance, any increase in the internal retail floorspace of 200sq m or more will be brought under planning contol, meaning that permission would have to be sought before supermarkets could make large internal changes to increase selling space.
The government maintained the new guidance has been introduced to boost local authorities' ability to promote the vitality of town centres.
ACS public affairs manager James Lowman explained: "We won the argument over mezzanine floors two years ago. In the meantime the large supermarkets have been able to create these areas unhindered. In many respects the damage has already been done."
Planning authorities will be given an extra five weeks to consider major projects to help gather local views. Under the old system, a developer could appeal in favour of their application after just eight weeks if the local council hadn't made a ruling.
The measures will come into force on May 10.