The three retailers were among the 2006 regional winners in the awards, which celebrate the best cheese counters in the business and are run in association with The Grocer.
Morrisons in Scunthorpe won the award for the north, Somerfield in Chesterfield won for the central region and Waitrose in Newbury for the south.
In the independent category, judges voted for Larners of Holt in the south, Deli on the Square for the central region and Valvona & Crolla for the north. Larners of Holt and Deli on the Square were regional winners in 2005 and 2004, while Valvona & Crolla was overall winner in 2004.
The regional winners will pick up their prizes on 5 September at a lunch at Café Royal in London, where the best cheese retailer in the country in two categories will be named.