According to The Mail on Sunday, there is no conspicuous Waterstones branding on the stores, which include ‘Southwold Books’ in the town of Southwold in Suffolk (above).
The other two stores are ‘Rye Books’ in Rye, East Sussex, and ‘Harpenden Books’ in Harpenden, Hertfordshire.
The Mail on Sunday carried quotes from local traders describing the move as "naughty" and "dishonest" but did not mention that it has been nearly a year since the opening of the most recent of the three stores.
Harpenden Books was opened in April 2016 and Southwold Books in 2014, according to book trade publication The Bookseller.
The newspaper claimed: "Shops in Southwold High Street are facing an average rise in business rates of 177% over the next five years. Many independent shopkeepers blame the arrival of national chains for pushing up rents, which in turn affects the rates."
The Mail on Sunday did not specify how the rates paid by the Waterstones stores were set to change.
James Daunt, managing director of Waterstones, told The Mail on Sunday that branding small shops as being independent helped them integrate with local communities in smaller towns.
He said it was part of his "crusade" to get the chain to behave like an independent bookseller, with each shop having its own identity.